None
**Instruments Affected**: NIRSpec
Tested on CV3 data
The library imports relevant to this notebook are aready taken care of by importing PTT.
NOTE: This notebook assumes that the pipeline version to be tested is already installed and its environment is activated.
To be able to run this notebook you need to install nptt.
If all goes well you will be able to import PTT.
# Create a temporary directory to hold notebook output, and change the working directory to that directory.
from tempfile import TemporaryDirectory
import os
import shutil
data_dir = TemporaryDirectory()
os.chdir(data_dir.name)
# Choose CRDS cache location
use_local_crds_cache = False
crds_cache_tempdir = False
crds_cache_notebook_dir = True
crds_cache_home = False
crds_cache_custom_dir = False
crds_cache_dir_name = ""
if use_local_crds_cache:
if crds_cache_tempdir:
os.environ['CRDS_PATH'] = os.path.join(os.getcwd(), "crds")
elif crds_cache_notebook_dir:
try:
os.environ['CRDS_PATH'] = os.path.join(orig_dir, "crds")
except Exception as e:
os.environ['CRDS_PATH'] = os.path.join(os.getcwd(), "crds")
elif crds_cache_home:
os.environ['CRDS_PATH'] = os.path.join(os.environ['HOME'], 'crds', 'cache')
elif crds_cache_custom_dir:
os.environ['CRDS_PATH'] = crds_cache_dir_name
import warnings
import psutil
from astropy.io import fits
# Only print a DeprecationWarning the first time it shows up, not every time.
with warnings.catch_warnings():
warnings.simplefilter("once", category=DeprecationWarning)
import jwst
from jwst.pipeline.calwebb_detector1 import Detector1Pipeline
from jwst.assign_wcs.assign_wcs_step import AssignWcsStep
from jwst.msaflagopen.msaflagopen_step import MSAFlagOpenStep
from jwst.extract_2d.extract_2d_step import Extract2dStep
from jwst.srctype.srctype_step import SourceTypeStep
from jwst.wavecorr.wavecorr_step import WavecorrStep
from jwst.flatfield.flat_field_step import FlatFieldStep
from jwst.pathloss.pathloss_step import PathLossStep
from jwst import datamodels
# The latest version of NPTT is installed in the requirements text file at:
# /jwst_validation_notebooks/environment.yml
# import NPTT
import nirspec_pipe_testing_tool as nptt
# To get data from Artifactory
from ci_watson.artifactory_helpers import get_bigdata
2021-05-17 22:22:50,842 - stpipe - WARNING - /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/photutils/detection/findstars.py:33: AstropyDeprecationWarning: _StarFinderKernel was moved to the photutils.detection._utils module. Please update your import statement.
warnings.warn(f'{name} was moved to the {deprecated[name]} module. '
# Make sure that the version used is the right one
pipeline_version = jwst.__version__
nptt_version = nptt.__version__
print("Using jwst pipeline version: ", pipeline_version)
print("Using NPTT version: ", nptt_version)
Using jwst pipeline version: 1.1.0 Using NPTT version: 1.1.14
The NIRSpec team developed an implementation of the pathloss step and compared the output to the pipeline output for this step. We expected machine precision differences (about 10^-7) but due to rounding differences in interpolation methods we relaxed the difference threshold to 10^-6.
For the test to be considered PASSED, every single slit (for FS data), slitlet (for MOS data) or slice (for IFU data) in the input file has to pass. If there is any failure, the whole test will be considered as FAILED.
The code for this test for Fixed Slits (FS) can be obtained from: https://github.com/spacetelescope/nirspec_pipe_testing_tool/blob/master/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_fs_ps.py. There is a corresponding script for Multi Object Spectroscopy (MOS) and for Integral Field Unit (IFU) data. Each mode has a script for point source (ps) and for uniform source (uni).
Step description: https://jwst-pipeline.readthedocs.io/en/latest/jwst/pathloss/description.html
Pipeline code: https://github.com/spacetelescope/jwst/tree/master/jwst/pathloss
If the test PASSED this means that all slits, slitlets, or slices individually passed the test. However, if ony one individual slit (for FS data), slitlet (for MOS data) or slice (for IFU data) test failed, the whole test will be reported as FAILED.
A short description and link to the page: https://outerspace.stsci.edu/display/JWSTCC/Vanilla+Spectral+GWCS+Information
Acronymns used un this notebook:
pipeline: calibration pipeline
spec2: spectroscopic calibration pipeline level 2b
PTT: NIRSpec pipeline testing tool (https://github.com/spacetelescope/nirspec_pipe_testing_tool)
The pipeline can be run from the command line in two variants: full or per step.
Tu run the spec2 pipeline in full use the command:
$ strun jwst.pipeline.Spec2Pipeline jwtest_rate.fits
Tu only run the pathloss step, use the command:
$ strun jwst.pathloss.PathLossStep jwtest_previous_step_output.fits
These options are also callable from a script with the testing environment active. The Python call for running the pipeline in full or by step are:
$\gt$ from jwst.pipeline.calwebb_spec2 import Spec2Pipeline
$\gt$ Spec2Pipeline.call(jwtest_rate.fits)
or
$\gt$ from jwst.pathloss import PathLossStep
$\gt$ PathLossStep.call(jwtest_previous_step_output.fits)
PTT can run the spec2 pipeline either in full or per step, as well as the imaging pipeline in full. In this notebook we will use PTT to run the pipeline and the validation tests. To run PTT, follow the directions in the corresponding repo page.
All testing data is from the CV3 campaign. We chose these files because this is our most complete data set, i.e. all modes and filter-grating combinations.
Data used was for testing was only FS and MOS, since extract_2d is skipped for IFU. Data sets are:
testing_data = {'fs_prism_clear':{
'uncal_file_nrs1': 'fs_prism_nrs1_uncal.fits',
'uncal_file_nrs2': 'fs_prism_nrs2_uncal.fits',
'msa_shutter_config': None },
'fs_fullframe_g395h_f290lp':{
'uncal_file_nrs1': 'fs_fullframe_g395h_f290lp_nrs1_uncal.fits',
'uncal_file_nrs2': 'fs_fullframe_g395h_f290lp_nrs2_uncal.fits',
'msa_shutter_config': None },
# Commented out because wavecor is failing with this data set
#'fs_allslits_g140h_f100lp':{
# 'uncal_file_nrs1': 'fs_allslits_g140h_f100lp_nrs1_uncal.fits',
# 'uncal_file_nrs2': 'fs_allslits_g140h_f100lp_nrs2_uncal.fits',
# 'msa_shutter_config': None },
# Commented out because wavecor is not populating array
#'bots_g235h_f170lp':{
# 'uncal_file_nrs1': 'bots_g235h_f170lp_nrs1_uncal.fits',
# 'uncal_file_nrs2': 'bots_g235h_f170lp_nrs2_uncal.fits',
# 'msa_shutter_config': None },
'mos_prism_clear':{
'uncal_file_nrs1': 'mos_prism_nrs1_uncal.fits',
'uncal_file_nrs2': 'mos_prism_nrs2_uncal.fits',
'msa_shutter_config': 'V0030006000104_msa.fits' },
'mos_g140m_f100lp':{
'uncal_file_nrs1': 'mos_g140m_line1_NRS1_uncal.fits',
'uncal_file_nrs2': 'mos_g140m_line1_NRS2_uncal.fits',
'msa_shutter_config': 'V8460001000101_msa.fits' },
'ifu_prism_clear':{
'uncal_file_nrs1': 'ifu_prism_nrs1_uncal.fits',
'uncal_file_nrs2': 'ifu_prism_nrs2_uncal.fits',
'msa_shutter_config': None },
'ifu_g395h_f290lp':{
'uncal_file_nrs1': 'ifu_g395h_f290lp_nrs1_uncal.fits',
'uncal_file_nrs2': 'ifu_g395h_f290lp_nrs2_uncal.fits',
'msa_shutter_config': None }
}
# define function to pull data from Artifactory
def get_artifactory_file(data_set_dict, detector):
"""This function creates a list with all the files needed per detector to run the test.
Args:
data_set_dict: dictionary, contains inputs for a specific mode and configuration
detector: string, either nrs1 or nrs2
Returns:
data: list, contains all files needed to run test
"""
files2obtain = ['uncal_file_nrs1', 'msa_shutter_config']
data = []
for file in files2obtain:
data_file = None
try:
if '_nrs' in file and '2' in detector:
file = file.replace('_nrs1', '_nrs2')
data_file = get_bigdata('jwst_validation_notebooks',
'validation_data',
'nirspec_data',
data_set_dict[file])
except TypeError:
data.append(None)
continue
data.append(data_file)
return data
# Set common NPTT switches for this test
# accepted threshold difference with respect to benchmark files
threshold_diff = 9.999e-05
# other NPTT variables
writefile = False
show_figs = True
save_figs = False
# Get the data
detectors = ['nrs1', 'nrs2']
results_dict = {}
for mode_config, data_set_dict in testing_data.items():
for det in detectors:
print('Testing files for detector: ', det)
data = get_artifactory_file(data_set_dict, det)
uncal_file, msa_shutter_config = data
print('Working with uncal_file: ', uncal_file)
uncal_basename = os.path.basename(uncal_file)
# Run the stage 1 pipeline
rate_object = Detector1Pipeline.call(uncal_file)
# Make sure the MSA shutter configuration file is set up correctly
rate_object.meta.instrument.msa_metadata_file = msa_shutter_config
if msa_shutter_config is not None:
msa_metadata = rate_object.meta.instrument.msa_metadata_file
print('MSA shutter configuration file: ', msa_metadata)
if msa_metadata is None or msa_metadata == 'N/A':
rate_object.meta.instrument.msa_metadata_file = msa_shutter_config
# Run the stage 2 pipeline steps
try:
pipe_object = AssignWcsStep.call(rate_object)
skip_file = False
except:
print('An error occurred that made the pipeline crash, probably: No open slits fall on detector ', det)
print("Skipping test for this file. \n")
skip_file = True
if not skip_file:
if 'ifu' in uncal_basename.lower() or 'mos' in uncal_basename.lower():
pipe_object = MSAFlagOpenStep.call(pipe_object)
if 'ifu' not in uncal_basename.lower():
pipe_object = Extract2dStep.call(pipe_object)
pipe_object = SourceTypeStep.call(pipe_object)
pipe_object = WavecorrStep.call(pipe_object)
flat_field_object = FlatFieldStep.call(pipe_object)
pathloss_object = PathLossStep.call(flat_field_object)
# get the corresponding reference file from the pathloss datamodel
reffile_path = pathloss_object.meta.ref_file.pathloss.name.replace("crds://",
"https://jwst-crds.stsci.edu/unchecked_get/references/jwst/")
# Run the validation test
%matplotlib inline
if 'fs' in uncal_file.lower():
print('Running test for FS...')
if pathloss_object.meta.target.source_type == 'POINT' or source_type is None:
median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_fs_ps.pathtest(
flat_field_object,
reffile_path,
pathloss_object,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff)
else:
median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_fs_uni.pathtest(
flat_field_object,
reffile_path,
pathloss_object,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff)
if 'mos' in uncal_file.lower():
print('Running test for MOS...')
median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_mos.pathtest(
flat_field_object,
reffile_path,
pathloss_object,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff)
if 'ifu' in uncal_file.lower():
print('Running test for IFU...')
if pathloss_object.meta.target.source_type == 'POINT':
median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_ifu_ps.pathtest(
flat_field_object,
reffile_path,
pathloss_object,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff)
else:
median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_ifu_uni.pathtest(
flat_field_object,
reffile_path,
pathloss_object,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff)
else:
result_msg = 'skipped'
# Did the test passed
print("Did pathloss validation test passed? ", result_msg, "\n\n")
rd = {mode_config: result_msg}
results_dict.update(rd)
# close all open files
psutil.Process().open_files()
closing_files = []
for fd in psutil.Process().open_files():
if data_dir.name in fd.path:
closing_files.append(fd)
for fd in closing_files:
try:
print('Closing file: ', fd)
open(fd.fd).close()
except:
print('File already closed: ', fd)
Testing files for detector: nrs1 Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_prism_nrs1_uncal.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.instrument.fixed_slit the following error occurred:
'FULL' is not one of ['S200A1', 'S200A2', 'S200B1', 'S400A1', 'S1600A1', 'NONE']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Name of fixed slit aperture used'),
('type', 'string'),
('enum',
['S200A1',
'S200A2',
'S200B1',
'S400A1',
'S1600A1',
'NONE']),
('fits_keyword', 'FXD_SLIT'),
('blend_table', True)])
On instance:
'FULL'
warnings.warn(errmsg, ValidationWarning)
2021-05-17 22:22:53,325 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:22:53,350 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:22:53,352 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:22:53,354 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:22:53,355 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:22:53,357 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:22:53,359 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:22:53,362 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:22:53,364 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:22:53,366 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:22:53,368 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:22:53,370 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:22:53,371 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:22:53,373 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:22:53,375 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:22:53,377 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:22:53,379 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:22:53,381 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2021-05-17 22:22:53,518 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_prism_nrs1_uncal.fits',).
2021-05-17 22:22:53,531 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:22:53,702 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'fs_prism_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:22:53,724 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits'.
2021-05-17 22:22:53,727 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2021-05-17 22:22:53,729 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits'.
2021-05-17 22:22:53,732 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2021-05-17 22:22:53,734 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:22:53,735 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2021-05-17 22:22:53,737 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits'.
2021-05-17 22:22:53,739 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:22:53,740 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:22:53,740 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits'.
2021-05-17 22:22:53,743 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits'.
2021-05-17 22:22:53,745 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:22:53,745 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:22:53,746 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:22:54,209 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:22:54,211 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:22:54,442 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:22:54,443 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:22:54,445 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:22:54,582 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:22:54,584 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:22:54,602 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2021-05-17 22:22:55,084 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:22:55,261 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:22:55,263 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:22:55,282 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits
2021-05-17 22:22:56,794 - stpipe.Detector1Pipeline.saturation - INFO - Detected 9869 saturated pixels
2021-05-17 22:22:56,844 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:22:56,881 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:22:57,054 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:22:57,056 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:22:57,057 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:22:57,059 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:22:57,225 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:22:57,227 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:22:57,247 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-05-17 22:23:04,096 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:23:04,260 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:23:04,262 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:23:04,282 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits
2021-05-17 22:23:19,737 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:23:20,097 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:23:20,100 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:23:20,122 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits
2021-05-17 22:23:23,646 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:23:23,807 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:23:23,809 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:23:23,871 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits
2021-05-17 22:24:12,521 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=4, nframes=1, groupgap=0
2021-05-17 22:24:12,524 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-05-17 22:24:13,274 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:24:13,940 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:13,942 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:24:13,987 - stpipe.Detector1Pipeline.jump - WARNING - Can not apply jump detection when NGROUPS<=4;
2021-05-17 22:24:13,988 - stpipe.Detector1Pipeline.jump - WARNING - Jump step will be skipped
2021-05-17 22:24:14,141 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:24:14,243 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:14,244 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:24:14,386 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-05-17 22:24:14,440 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-05-17 22:24:15,112 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:24:15,113 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2021-05-17 22:24:27,769 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 4
2021-05-17 22:24:27,772 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:1091: RuntimeWarning: divide by zero encountered in true_divide
var_p2 = 1/(s_inv_var_p3.sum(axis=0))
2021-05-17 22:24:27,905 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:24:28,132 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:28,135 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:24:28,212 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:24:28,214 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:24:28,217 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:24:28,383 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:28,387 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:24:28,456 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:24:28,457 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:24:28,460 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:24:28,461 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:24:28,463 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:24:28,472 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:24:28,707 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:28,709 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 22:24:28,890 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-05-17 22:24:28,891 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-05-17 22:24:28,892 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-05-17 22:24:28,893 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:24:29,250 - stpipe.AssignWcsStep - INFO - Removing slit S200B1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:24:29,251 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: ['S200A1', 'S200A2', 'S400A1', 'S1600A1']
2021-05-17 22:24:29,251 - stpipe.AssignWcsStep - INFO - Computing WCS for 4 open slitlets
2021-05-17 22:24:29,279 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-05-17 22:24:29,279 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-05-17 22:24:29,280 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-05-17 22:24:29,281 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:24:29,290 - stpipe.AssignWcsStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-05-17 22:24:29,417 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 1
2021-05-17 22:24:29,418 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2021-05-17 22:24:29,419 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 3
2021-05-17 22:24:29,420 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 4
2021-05-17 22:24:29,420 - stpipe.AssignWcsStep - INFO - There are 4 open slits in quadrant 5
2021-05-17 22:24:29,606 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_fixedslit pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2021-05-17 22:24:29,905 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 22:24:29,911 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 22:24:29,920 - stpipe.Extract2dStep - INFO - Extract2dStep instance created.
2021-05-17 22:24:30,006 - stpipe.Extract2dStep - INFO - Step Extract2dStep running with args (<ImageModel(2048, 2048) from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:30,008 - stpipe.Extract2dStep - INFO - Step Extract2dStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'grism_objects': None, 'mmag_extract': 99.0}
2021-05-17 22:24:30,023 - stpipe.Extract2dStep - INFO - EXP_TYPE is NRS_FIXEDSLIT
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/utils.py:72: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
indx = np.asarray(np.floor(np.asarray(value) + 0.5), dtype=np.int)
2021-05-17 22:24:30,234 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S200A1
2021-05-17 22:24:30,235 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1083 1518
2021-05-17 22:24:30,235 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1056 1096
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 22:24:30,362 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:24:30,371 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.191685737 -45.682908511 156.190837415 -45.682092120 156.190771015 -45.682126390 156.191619323 -45.682942792
2021-05-17 22:24:30,372 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.191685737 -45.682908511 156.190837415 -45.682092120 156.190771015 -45.682126390 156.191619323 -45.682942792
2021-05-17 22:24:30,536 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S200A2
2021-05-17 22:24:30,537 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 892 1328
2021-05-17 22:24:30,538 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1020 1060
2021-05-17 22:24:30,662 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:24:30,671 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.184519149 -45.685298792 156.183675453 -45.684484578 156.183609578 -45.684518640 156.184453260 -45.685332865
2021-05-17 22:24:30,672 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.184519149 -45.685298792 156.183675453 -45.684484578 156.183609578 -45.684518640 156.184453260 -45.685332865
2021-05-17 22:24:30,948 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S400A1
2021-05-17 22:24:30,948 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1025 1460
2021-05-17 22:24:30,949 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 979 1024
2021-05-17 22:24:31,072 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:24:31,082 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.187759056 -45.682331806 156.186793281 -45.681401531 156.186663358 -45.681468621 156.187629101 -45.682398919
2021-05-17 22:24:31,082 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.187759056 -45.682331806 156.186793281 -45.681401531 156.186663358 -45.681468621 156.187629101 -45.682398919
2021-05-17 22:24:31,243 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S1600A1
2021-05-17 22:24:31,243 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1056 1488
2021-05-17 22:24:31,244 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 959 982
2021-05-17 22:24:31,370 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:24:31,380 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.187720636 -45.680802803 156.187307671 -45.680405209 156.186792650 -45.680671077 156.187205560 -45.681068709
2021-05-17 22:24:31,381 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.187720636 -45.680802803 156.187307671 -45.680405209 156.186792650 -45.680671077 156.187205560 -45.681068709
2021-05-17 22:24:31,507 - stpipe.Extract2dStep - INFO - Step Extract2dStep done
2021-05-17 22:24:31,894 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 22:24:32,021 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<MultiSlitModel from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:32,023 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:24:32,030 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_FIXEDSLIT
2021-05-17 22:24:32,031 - stpipe.SourceTypeStep - INFO - Input SRCTYAPT = UNKNOWN
2021-05-17 22:24:32,031 - stpipe.SourceTypeStep - INFO - Input source type is unknown; setting default SRCTYPE = POINT
2021-05-17 22:24:32,035 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 22:24:32,051 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 22:24:32,151 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<MultiSlitModel from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:32,152 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:24:32,176 - stpipe.WavecorrStep - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0001.asdf
2021-05-17 22:24:32,648 - stpipe.WavecorrStep - WARNING - Primary slit name not found in input
2021-05-17 22:24:32,649 - stpipe.WavecorrStep - WARNING - Skipping wavecorr correction
2021-05-17 22:24:32,652 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 22:24:32,667 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 22:24:32,792 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<MultiSlitModel from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:32,793 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 22:24:35,102 - stpipe.FlatFieldStep - INFO - Working on slit S200A1
2021-05-17 22:24:38,678 - stpipe.FlatFieldStep - INFO - Working on slit S200A2
2021-05-17 22:24:42,368 - stpipe.FlatFieldStep - INFO - Working on slit S400A1
2021-05-17 22:24:46,281 - stpipe.FlatFieldStep - INFO - Working on slit S1600A1
2021-05-17 22:24:48,215 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 22:24:48,231 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 22:24:48,429 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<MultiSlitModel from fs_prism_nrs1_uncal.fits>,).
2021-05-17 22:24:48,431 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 22:24:48,456 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0001.fits
2021-05-17 22:24:48,546 - stpipe.PathLossStep - INFO - Input exposure type is NRS_FIXEDSLIT
2021-05-17 22:24:49,045 - stpipe.PathLossStep - INFO - Working on slit S200A1
2021-05-17 22:24:49,046 - stpipe.PathLossStep - INFO - Using aperture S200A1
2021-05-17 22:24:49,065 - stpipe.PathLossStep - INFO - Working on slit S200A2
2021-05-17 22:24:49,066 - stpipe.PathLossStep - INFO - Using aperture S200A2
2021-05-17 22:24:49,084 - stpipe.PathLossStep - INFO - Working on slit S400A1
2021-05-17 22:24:49,084 - stpipe.PathLossStep - WARNING - Cannot find matching pathloss model for S400A1
2021-05-17 22:24:49,085 - stpipe.PathLossStep - WARNING - Skipping pathloss correction for this slit
2021-05-17 22:24:49,086 - stpipe.PathLossStep - WARNING - No correction provided for slit 2. Skipping
2021-05-17 22:24:49,086 - stpipe.PathLossStep - INFO - Working on slit S1600A1
2021-05-17 22:24:49,087 - stpipe.PathLossStep - INFO - Using aperture S1600A1
2021-05-17 22:24:49,107 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for FS...
Checking if files exist and obtaining datamodels. This takes a few minutes...
from datamodel --> Detector: NRS1 Grating: PRISM Filter: CLEAR Lamp: LINE4 EXP_TYPE: NRS_FIXEDSLIT
Now looping through the slits. This may take a while...
Looping through the wavelengths...
Working with slitlet S200A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
Calculating statistics...
Absolute Difference : mean = -1.096e-16 median = -2.220e-16 stdev = 3.665e-16
Maximum AbsoluteDifference = 8.882e-16
Minimum AbsoluteDifference = -4.441e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet S200A2
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_fs_ps.py:304: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/aa0c667e23a747249d9442a76121955c/contents' mode='rb' closefd=True> hdul = fits.open(reffile2use)
<Figure size 432x288 with 0 Axes>
Calculating statistics...
Absolute Difference : mean = -1.122e-16 median = -2.220e-16 stdev = 3.646e-16
Maximum AbsoluteDifference = 8.882e-16
Minimum AbsoluteDifference = -4.441e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet S400A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Unable to retrieve extension.
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
Pipeline pathloss correction in datamodel is empty. Skipping testing this slit.
Working with slitlet S1600A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
<Figure size 432x288 with 0 Axes>
Calculating statistics...
Absolute Difference : mean = -1.288e-16 median = -2.220e-16 stdev = 1.365e-16
Maximum AbsoluteDifference = 2.220e-16
Minimum AbsoluteDifference = -2.220e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final pathloss test result reported as PASSED ***
('* Script FS_PS.py took ', '3.870344849427541 minutes to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
Testing files for detector: nrs2
<ipython-input-1-c1525cc413af>:62: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/aa0c667e23a747249d9442a76121955c/contents' mode='rb' closefd=True> median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_fs_ps.pathtest(
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_prism_nrs2_uncal.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.instrument.fixed_slit the following error occurred:
'FULL' is not one of ['S200A1', 'S200A2', 'S200B1', 'S400A1', 'S1600A1', 'NONE']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Name of fixed slit aperture used'),
('type', 'string'),
('enum',
['S200A1',
'S200A2',
'S200B1',
'S400A1',
'S1600A1',
'NONE']),
('fits_keyword', 'FXD_SLIT'),
('blend_table', True)])
On instance:
'FULL'
warnings.warn(errmsg, ValidationWarning)
2021-05-17 22:28:42,378 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:28:42,395 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:28:42,396 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:28:42,398 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:28:42,400 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:28:42,401 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:28:42,402 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:28:42,404 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:28:42,405 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:28:42,407 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:28:42,408 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:28:42,410 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:28:42,411 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:28:42,412 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:28:42,414 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:28:42,415 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:28:42,417 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:28:42,419 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_prism_nrs2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 22:28:42,751 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_prism_nrs2_uncal.fits',).
2021-05-17 22:28:42,761 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:28:42,877 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'fs_prism_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:28:42,896 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0087.fits'.
2021-05-17 22:28:42,899 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits'.
2021-05-17 22:28:42,901 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits'.
2021-05-17 22:28:42,904 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits'.
2021-05-17 22:28:42,906 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:28:42,907 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits'.
2021-05-17 22:28:42,909 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0020.fits'.
2021-05-17 22:28:42,912 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:28:42,913 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:28:42,914 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits'.
2021-05-17 22:28:42,916 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0114.fits'.
2021-05-17 22:28:42,918 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:28:42,919 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:28:42,920 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:28:43,496 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:28:43,499 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:28:43,674 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:28:43,675 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:28:43,677 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:28:43,940 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:28:43,942 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:28:43,964 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits
2021-05-17 22:28:44,397 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:28:44,665 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:28:44,668 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:28:44,687 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits
2021-05-17 22:28:45,383 - stpipe.Detector1Pipeline.saturation - INFO - Detected 5379 saturated pixels
2021-05-17 22:28:45,408 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:28:45,434 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:28:45,733 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:28:45,735 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:28:45,736 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:28:45,738 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:28:45,990 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:28:45,992 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:28:46,017 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0114.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-05-17 22:28:50,606 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:28:50,779 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:28:50,781 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:28:50,802 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0020.fits
2021-05-17 22:29:06,999 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:29:07,350 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:07,352 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:29:07,373 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits
2021-05-17 22:29:08,215 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:29:08,388 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:08,390 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:29:08,466 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0087.fits
2021-05-17 22:29:41,380 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=4, nframes=1, groupgap=0
2021-05-17 22:29:41,381 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-05-17 22:29:42,069 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:29:42,711 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:42,713 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:29:42,748 - stpipe.Detector1Pipeline.jump - WARNING - Can not apply jump detection when NGROUPS<=4;
2021-05-17 22:29:42,749 - stpipe.Detector1Pipeline.jump - WARNING - Jump step will be skipped
2021-05-17 22:29:42,903 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:29:43,046 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 4, 3200, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:43,048 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:29:43,188 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-05-17 22:29:43,236 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-05-17 22:29:43,293 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:29:43,294 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2021-05-17 22:29:55,509 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 4
2021-05-17 22:29:55,511 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:1091: RuntimeWarning: divide by zero encountered in true_divide
var_p2 = 1/(s_inv_var_p3.sum(axis=0))
2021-05-17 22:29:55,684 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:29:55,968 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:55,971 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:29:56,035 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:29:56,036 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:29:56,040 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:29:56,308 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:56,311 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:29:56,377 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:29:56,378 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:29:56,382 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:29:56,383 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:29:56,385 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:29:56,395 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:29:56,677 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:56,679 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 22:29:56,852 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-05-17 22:29:56,853 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-05-17 22:29:56,854 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-05-17 22:29:56,856 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:29:57,065 - stpipe.AssignWcsStep - INFO - Removing slit S200A1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:29:57,105 - stpipe.AssignWcsStep - INFO - Removing slit S200A2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:29:57,146 - stpipe.AssignWcsStep - INFO - Removing slit S400A1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:29:57,186 - stpipe.AssignWcsStep - INFO - Removing slit S1600A1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:29:57,226 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS2: ['S200B1']
2021-05-17 22:29:57,227 - stpipe.AssignWcsStep - INFO - Computing WCS for 1 open slitlets
2021-05-17 22:29:57,256 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-05-17 22:29:57,257 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-05-17 22:29:57,257 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-05-17 22:29:57,259 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:29:57,268 - stpipe.AssignWcsStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-05-17 22:29:57,387 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 1
2021-05-17 22:29:57,388 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2021-05-17 22:29:57,389 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 3
2021-05-17 22:29:57,390 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 4
2021-05-17 22:29:57,391 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 5
2021-05-17 22:29:57,520 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_fixedslit pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2021-05-17 22:29:57,684 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 22:29:57,693 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 22:29:57,703 - stpipe.Extract2dStep - INFO - Extract2dStep instance created.
2021-05-17 22:29:58,006 - stpipe.Extract2dStep - INFO - Step Extract2dStep running with args (<ImageModel(2048, 2048) from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:58,009 - stpipe.Extract2dStep - INFO - Step Extract2dStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'grism_objects': None, 'mmag_extract': 99.0}
2021-05-17 22:29:58,027 - stpipe.Extract2dStep - INFO - EXP_TYPE is NRS_FIXEDSLIT
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/utils.py:72: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
indx = np.asarray(np.floor(np.asarray(value) + 0.5), dtype=np.int)
2021-05-17 22:29:58,177 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S200B1
2021-05-17 22:29:58,178 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 440 864
2021-05-17 22:29:58,179 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 918 962
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 22:29:58,329 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:29:58,339 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.238745821 -45.653926065 156.237887188 -45.653118339 156.237822146 -45.653151380 156.238680762 -45.653959111
2021-05-17 22:29:58,340 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.238745821 -45.653926065 156.237887188 -45.653118339 156.237822146 -45.653151380 156.238680762 -45.653959111
2021-05-17 22:29:58,376 - stpipe.Extract2dStep - INFO - Step Extract2dStep done
2021-05-17 22:29:58,390 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 22:29:58,660 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<MultiSlitModel from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:58,662 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:29:58,671 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_FIXEDSLIT
2021-05-17 22:29:58,672 - stpipe.SourceTypeStep - INFO - Input SRCTYAPT = UNKNOWN
2021-05-17 22:29:58,673 - stpipe.SourceTypeStep - INFO - Input source type is unknown; setting default SRCTYPE = POINT
2021-05-17 22:29:58,675 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 22:29:58,687 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 22:29:58,932 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<MultiSlitModel from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:58,934 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:29:58,954 - stpipe.WavecorrStep - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0001.asdf
2021-05-17 22:29:59,132 - stpipe.WavecorrStep - WARNING - Primary slit name not found in input
2021-05-17 22:29:59,133 - stpipe.WavecorrStep - WARNING - Skipping wavecorr correction
2021-05-17 22:29:59,137 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 22:29:59,151 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 22:29:59,414 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<MultiSlitModel from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:29:59,416 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 22:30:02,036 - stpipe.FlatFieldStep - INFO - Working on slit S200B1
2021-05-17 22:30:05,492 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 22:30:05,504 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 22:30:05,784 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<MultiSlitModel from fs_prism_nrs2_uncal.fits>,).
2021-05-17 22:30:05,786 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 22:30:05,808 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0001.fits
2021-05-17 22:30:05,879 - stpipe.PathLossStep - INFO - Input exposure type is NRS_FIXEDSLIT
2021-05-17 22:30:06,063 - stpipe.PathLossStep - INFO - Working on slit S200B1
2021-05-17 22:30:06,064 - stpipe.PathLossStep - INFO - Using aperture S200B1
2021-05-17 22:30:06,087 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for FS...
Checking if files exist and obtaining datamodels. This takes a few minutes...
from datamodel --> Detector: NRS2 Grating: PRISM Filter: CLEAR Lamp: LINE4 EXP_TYPE: NRS_FIXEDSLIT
Now looping through the slits. This may take a while...
Looping through the wavelengths...
Working with slitlet S200B1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
Calculating statistics...
Absolute Difference : mean = -1.143e-16 median = -2.220e-16 stdev = 3.639e-16
Maximum AbsoluteDifference = 8.882e-16
Minimum AbsoluteDifference = -4.441e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final pathloss test result reported as PASSED ***
('* Script FS_PS.py took ', '1.0635647813479105 minutes to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
Testing files for detector: nrs1
<ipython-input-1-c1525cc413af>:62: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/aa0c667e23a747249d9442a76121955c/contents' mode='rb' closefd=True> median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_fs_ps.pathtest(
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_fullframe_g395h_f290lp_nrs1_uncal.fits
2021-05-17 22:31:11,854 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:31:11,873 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:31:11,875 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:31:11,876 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:31:11,877 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:31:11,879 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:31:11,880 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:31:11,882 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:31:11,883 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:31:11,885 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:31:11,886 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:31:11,888 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:31:11,889 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:31:11,890 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:31:11,892 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:31:11,893 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:31:11,895 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:31:11,896 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_fullframe_g395h_f290lp_nrs1_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 22:31:12,111 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_fullframe_g395h_f290lp_nrs1_uncal.fits',).
2021-05-17 22:31:12,122 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:31:12,271 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'fs_fullframe_g395h_f290lp_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:31:12,284 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits'.
2021-05-17 22:31:12,287 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2021-05-17 22:31:12,290 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits'.
2021-05-17 22:31:12,294 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2021-05-17 22:31:12,297 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:31:12,298 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2021-05-17 22:31:12,302 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits'.
2021-05-17 22:31:12,305 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:31:12,306 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:31:12,307 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits'.
2021-05-17 22:31:12,310 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits'.
2021-05-17 22:31:12,314 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:31:12,315 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:31:12,316 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:31:12,761 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:12,763 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:31:13,017 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:31:13,018 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:31:13,020 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:31:13,219 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:13,221 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:31:13,242 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2021-05-17 22:31:13,788 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:31:14,005 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:14,006 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:31:14,026 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits
2021-05-17 22:31:15,041 - stpipe.Detector1Pipeline.saturation - INFO - Detected 11377 saturated pixels
2021-05-17 22:31:15,120 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:31:15,155 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:31:15,413 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:15,415 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:31:15,415 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:31:15,417 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:31:15,628 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:15,630 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:31:15,651 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-05-17 22:31:16,259 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:31:16,477 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:16,479 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:31:16,499 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits
2021-05-17 22:31:38,414 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:31:38,857 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:38,860 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:31:38,884 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits
2021-05-17 22:31:39,986 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:31:40,233 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:40,235 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:31:40,337 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits
2021-05-17 22:31:44,584 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=7, nframes=1, groupgap=0
2021-05-17 22:31:44,585 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-05-17 22:31:45,248 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:31:46,127 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:46,129 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:31:46,180 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-05-17 22:31:46,235 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-05-17 22:31:46,376 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-05-17 22:31:46,435 - stpipe.Detector1Pipeline.jump - INFO - Found 32 possible cores to use for jump detection
2021-05-17 22:31:46,852 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-05-17 22:31:47,152 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-05-17 22:31:48,657 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 88509 pixels with at least one CR
2021-05-17 22:31:51,179 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 4.32609 sec
2021-05-17 22:31:51,183 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 5.003271
2021-05-17 22:31:51,186 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:31:51,427 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:31:51,429 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:31:51,539 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-05-17 22:31:51,586 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-05-17 22:31:51,632 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:31:51,633 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:872: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int,:,:,:] *= ( segs_4[num_int,:,:,:] > 0)
2021-05-17 22:32:24,305 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 7
2021-05-17 22:32:24,306 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-05-17 22:32:24,479 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:32:24,672 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:32:24,674 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:32:24,745 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:32:24,746 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:32:24,749 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:32:24,861 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:32:24,863 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:32:24,923 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:32:24,924 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:32:24,927 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:32:24,929 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:32:24,931 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:32:24,941 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:32:25,061 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:32:25,063 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 22:32:25,228 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-05-17 22:32:25,229 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-05-17 22:32:25,231 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-05-17 22:32:25,232 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:32:25,465 - stpipe.AssignWcsStep - INFO - Removing slit S200B1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:32:25,467 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: ['S200A1', 'S200A2', 'S400A1', 'S1600A1']
2021-05-17 22:32:25,467 - stpipe.AssignWcsStep - INFO - Computing WCS for 4 open slitlets
2021-05-17 22:32:25,495 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-05-17 22:32:25,496 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-05-17 22:32:25,497 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-05-17 22:32:25,498 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:32:25,508 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2021-05-17 22:32:25,625 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 1
2021-05-17 22:32:25,626 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2021-05-17 22:32:25,627 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 3
2021-05-17 22:32:25,628 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 4
2021-05-17 22:32:25,628 - stpipe.AssignWcsStep - INFO - There are 4 open slits in quadrant 5
2021-05-17 22:32:25,784 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_fixedslit pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2021-05-17 22:32:25,938 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 22:32:25,944 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 22:32:25,954 - stpipe.Extract2dStep - INFO - Extract2dStep instance created.
2021-05-17 22:32:26,090 - stpipe.Extract2dStep - INFO - Step Extract2dStep running with args (<ImageModel(2048, 2048) from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:32:26,093 - stpipe.Extract2dStep - INFO - Step Extract2dStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'grism_objects': None, 'mmag_extract': 99.0}
2021-05-17 22:32:26,109 - stpipe.Extract2dStep - INFO - EXP_TYPE is NRS_FIXEDSLIT
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/utils.py:72: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
indx = np.asarray(np.floor(np.asarray(value) + 0.5), dtype=np.int)
2021-05-17 22:32:26,272 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S200A1
2021-05-17 22:32:26,273 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 823 2048
2021-05-17 22:32:26,274 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1060 1122
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 22:32:26,452 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:32:26,461 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.191685737 -45.682908511 156.190837415 -45.682092120 156.190771015 -45.682126390 156.191619323 -45.682942792
2021-05-17 22:32:26,461 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.191685737 -45.682908511 156.190837415 -45.682092120 156.190771015 -45.682126390 156.191619323 -45.682942792
2021-05-17 22:32:26,609 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S200A2
2021-05-17 22:32:26,610 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 633 2048
2021-05-17 22:32:26,611 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1023 1081
2021-05-17 22:32:26,784 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:32:26,793 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.184519149 -45.685298792 156.183675453 -45.684484578 156.183609578 -45.684518640 156.184453260 -45.685332865
2021-05-17 22:32:26,793 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.184519149 -45.685298792 156.183675453 -45.684484578 156.183609578 -45.684518640 156.184453260 -45.685332865
2021-05-17 22:32:26,942 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S400A1
2021-05-17 22:32:26,943 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 751 2048
2021-05-17 22:32:26,944 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 983 1049
2021-05-17 22:32:27,358 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:32:27,368 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.187759056 -45.682331806 156.186793281 -45.681401531 156.186663358 -45.681468621 156.187629101 -45.682398919
2021-05-17 22:32:27,369 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.187759056 -45.682331806 156.186793281 -45.681401531 156.186663358 -45.681468621 156.187629101 -45.682398919
2021-05-17 22:32:27,522 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S1600A1
2021-05-17 22:32:27,523 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 774 2048
2021-05-17 22:32:27,524 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 964 1006
2021-05-17 22:32:27,675 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:32:27,684 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.187720636 -45.680802803 156.187307671 -45.680405209 156.186792650 -45.680671077 156.187205560 -45.681068709
2021-05-17 22:32:27,684 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.187720636 -45.680802803 156.187307671 -45.680405209 156.186792650 -45.680671077 156.187205560 -45.681068709
2021-05-17 22:32:27,808 - stpipe.Extract2dStep - INFO - Step Extract2dStep done
2021-05-17 22:32:27,828 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 22:32:28,086 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<MultiSlitModel from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:32:28,089 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:32:28,096 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_FIXEDSLIT
2021-05-17 22:32:28,097 - stpipe.SourceTypeStep - INFO - Input SRCTYAPT = UNKNOWN
2021-05-17 22:32:28,098 - stpipe.SourceTypeStep - INFO - Input source type is unknown; setting default SRCTYPE = POINT
2021-05-17 22:32:28,101 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 22:32:28,117 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 22:32:28,331 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<MultiSlitModel from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:32:28,333 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:32:28,357 - stpipe.WavecorrStep - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0001.asdf
2021-05-17 22:32:28,856 - stpipe.WavecorrStep - INFO - Detected a POINT source type in slit S200A1
2021-05-17 22:32:28,861 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:32:29,130 - stpipe.WavecorrStep - INFO - Using wavelength zero-point correction for aperture S200A1
2021-05-17 22:32:29,142 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 22:32:29,159 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 22:32:29,436 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<MultiSlitModel from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:32:29,439 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 22:32:31,753 - stpipe.FlatFieldStep - INFO - Working on slit S200A1
2021-05-17 22:32:31,755 - stpipe.FlatFieldStep - INFO - Creating wavelength array from WCS for slit S200A1
2021-05-17 22:32:50,191 - stpipe.FlatFieldStep - INFO - Working on slit S200A2
2021-05-17 22:33:01,440 - stpipe.FlatFieldStep - INFO - Working on slit S400A1
2021-05-17 22:33:13,248 - stpipe.FlatFieldStep - INFO - Working on slit S1600A1
2021-05-17 22:33:18,515 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 22:33:18,536 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 22:33:18,805 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<MultiSlitModel from fs_fullframe_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 22:33:18,807 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 22:33:18,831 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0001.fits
2021-05-17 22:33:18,896 - stpipe.PathLossStep - INFO - Input exposure type is NRS_FIXEDSLIT
2021-05-17 22:33:19,406 - stpipe.PathLossStep - INFO - Working on slit S200A1
2021-05-17 22:33:19,408 - stpipe.PathLossStep - INFO - Using aperture S200A1
2021-05-17 22:33:19,430 - stpipe.PathLossStep - INFO - Working on slit S200A2
2021-05-17 22:33:19,431 - stpipe.PathLossStep - INFO - Using aperture S200A2
2021-05-17 22:33:19,453 - stpipe.PathLossStep - INFO - Working on slit S400A1
2021-05-17 22:33:19,454 - stpipe.PathLossStep - WARNING - Cannot find matching pathloss model for S400A1
2021-05-17 22:33:19,455 - stpipe.PathLossStep - WARNING - Skipping pathloss correction for this slit
2021-05-17 22:33:19,456 - stpipe.PathLossStep - WARNING - No correction provided for slit 2. Skipping
2021-05-17 22:33:19,456 - stpipe.PathLossStep - INFO - Working on slit S1600A1
2021-05-17 22:33:19,457 - stpipe.PathLossStep - INFO - Using aperture S1600A1
2021-05-17 22:33:19,479 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for FS...
Checking if files exist and obtaining datamodels. This takes a few minutes...
from datamodel --> Detector: NRS1 Grating: G395H Filter: F290LP Lamp: LINE3 EXP_TYPE: NRS_FIXEDSLIT
Now looping through the slits. This may take a while...
Looping through the wavelengths...
Working with slitlet S200A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
Calculating statistics...
Absolute Difference : mean = -1.668e-16 median = -2.220e-16 stdev = 9.602e-17
Maximum AbsoluteDifference = 0.000e+00
Minimum AbsoluteDifference = -2.220e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet S200A2
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_fs_ps.py:304: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/aa0c667e23a747249d9442a76121955c/contents' mode='rb' closefd=True> hdul = fits.open(reffile2use)
<Figure size 432x288 with 0 Axes>
Calculating statistics...
Absolute Difference : mean = -1.848e-16 median = -2.220e-16 stdev = 1.074e-16
Maximum AbsoluteDifference = 0.000e+00
Minimum AbsoluteDifference = -4.441e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet S400A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Unable to retrieve extension.
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
Pipeline pathloss correction in datamodel is empty. Skipping testing this slit.
Working with slitlet S1600A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
<Figure size 432x288 with 0 Axes>
Calculating statistics...
Absolute Difference : mean = -1.084e-16 median = 0.000e+00 stdev = 1.110e-16
Maximum AbsoluteDifference = 0.000e+00
Minimum AbsoluteDifference = -2.220e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final pathloss test result reported as PASSED ***
('* Script FS_PS.py took ', '2.689649927616119 minutes to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
Testing files for detector: nrs2
<ipython-input-1-c1525cc413af>:62: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/aa0c667e23a747249d9442a76121955c/contents' mode='rb' closefd=True> median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_fs_ps.pathtest(
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_fullframe_g395h_f290lp_nrs2_uncal.fits
2021-05-17 22:36:02,454 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:36:02,470 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:36:02,471 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:36:02,472 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:36:02,474 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:36:02,475 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:36:02,476 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:36:02,477 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:36:02,479 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:36:02,480 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:36:02,481 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:36:02,482 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:36:02,483 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:36:02,485 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:36:02,486 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:36:02,487 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:36:02,489 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:36:02,490 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_fullframe_g395h_f290lp_nrs2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 22:36:02,708 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/fs_fullframe_g395h_f290lp_nrs2_uncal.fits',).
2021-05-17 22:36:02,718 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:36:02,873 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'fs_fullframe_g395h_f290lp_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:36:02,882 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0087.fits'.
2021-05-17 22:36:02,884 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits'.
2021-05-17 22:36:02,886 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits'.
2021-05-17 22:36:02,888 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits'.
2021-05-17 22:36:02,890 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:36:02,890 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits'.
2021-05-17 22:36:02,892 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0020.fits'.
2021-05-17 22:36:02,895 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:36:02,896 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:36:02,897 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits'.
2021-05-17 22:36:02,899 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0114.fits'.
2021-05-17 22:36:02,902 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:36:02,902 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:36:02,903 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:36:03,371 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:03,372 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:36:03,565 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:36:03,566 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:36:03,568 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:36:03,700 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:03,701 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:36:03,720 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits
2021-05-17 22:36:04,289 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:36:04,426 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:04,428 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:36:04,446 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits
2021-05-17 22:36:05,330 - stpipe.Detector1Pipeline.saturation - INFO - Detected 6420 saturated pixels
2021-05-17 22:36:05,411 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:36:05,437 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:36:05,575 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:05,577 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:36:05,577 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:36:05,579 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:36:05,707 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:05,708 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:36:05,727 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0114.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-05-17 22:36:06,208 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:36:06,345 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:06,346 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:36:06,365 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0020.fits
2021-05-17 22:36:28,489 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:36:28,797 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:28,799 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:36:28,819 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits
2021-05-17 22:36:29,769 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:36:29,915 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:29,917 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:36:30,001 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0087.fits
2021-05-17 22:36:34,196 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=7, nframes=1, groupgap=0
2021-05-17 22:36:34,197 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-05-17 22:36:34,768 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:36:35,524 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:35,526 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:36:35,573 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-05-17 22:36:35,621 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-05-17 22:36:35,723 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-05-17 22:36:35,774 - stpipe.Detector1Pipeline.jump - INFO - Found 32 possible cores to use for jump detection
2021-05-17 22:36:36,166 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-05-17 22:36:36,461 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-05-17 22:36:37,951 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 47875 pixels with at least one CR
2021-05-17 22:36:39,417 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 3.24975 sec
2021-05-17 22:36:39,420 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 3.846970
2021-05-17 22:36:39,423 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:36:39,557 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 7, 3200, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:36:39,559 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:36:39,658 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-05-17 22:36:39,704 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-05-17 22:36:39,746 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:36:39,747 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:872: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int,:,:,:] *= ( segs_4[num_int,:,:,:] > 0)
2021-05-17 22:37:10,915 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 7
2021-05-17 22:37:10,916 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-05-17 22:37:11,025 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:37:11,196 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:37:11,200 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:37:11,272 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:37:11,273 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:37:11,276 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:37:11,409 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:37:11,410 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:37:11,467 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:37:11,468 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:37:11,470 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:37:11,471 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:37:11,472 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:37:11,481 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:37:11,647 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:37:11,649 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 22:37:11,819 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-05-17 22:37:11,821 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-05-17 22:37:11,822 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-05-17 22:37:11,823 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:37:12,057 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS2: ['S200A1', 'S200A2', 'S400A1', 'S1600A1', 'S200B1']
2021-05-17 22:37:12,058 - stpipe.AssignWcsStep - INFO - Computing WCS for 5 open slitlets
2021-05-17 22:37:12,085 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-05-17 22:37:12,086 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-05-17 22:37:12,087 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-05-17 22:37:12,088 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:37:12,097 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2021-05-17 22:37:12,217 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 1
2021-05-17 22:37:12,218 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2021-05-17 22:37:12,219 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 3
2021-05-17 22:37:12,220 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 4
2021-05-17 22:37:12,220 - stpipe.AssignWcsStep - INFO - There are 5 open slits in quadrant 5
2021-05-17 22:37:12,388 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_fixedslit pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2021-05-17 22:37:12,548 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 22:37:12,555 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 22:37:12,564 - stpipe.Extract2dStep - INFO - Extract2dStep instance created.
2021-05-17 22:37:12,746 - stpipe.Extract2dStep - INFO - Step Extract2dStep running with args (<ImageModel(2048, 2048) from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:37:12,748 - stpipe.Extract2dStep - INFO - Step Extract2dStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'grism_objects': None, 'mmag_extract': 99.0}
2021-05-17 22:37:12,763 - stpipe.Extract2dStep - INFO - EXP_TYPE is NRS_FIXEDSLIT
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/utils.py:72: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
indx = np.asarray(np.floor(np.asarray(value) + 0.5), dtype=np.int)
2021-05-17 22:37:12,940 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S200A1
2021-05-17 22:37:12,941 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 2048
2021-05-17 22:37:12,942 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1060 1122
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 22:37:13,153 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:37:13,161 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.191685737 -45.682908511 156.190837415 -45.682092120 156.190771015 -45.682126390 156.191619323 -45.682942792
2021-05-17 22:37:13,162 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.191685737 -45.682908511 156.190837415 -45.682092120 156.190771015 -45.682126390 156.191619323 -45.682942792
2021-05-17 22:37:13,321 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S200A2
2021-05-17 22:37:13,322 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 2048
2021-05-17 22:37:13,322 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1023 1081
2021-05-17 22:37:13,517 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:37:13,526 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.184519149 -45.685298792 156.183675453 -45.684484578 156.183609578 -45.684518640 156.184453260 -45.685332865
2021-05-17 22:37:13,526 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.184519149 -45.685298792 156.183675453 -45.684484578 156.183609578 -45.684518640 156.184453260 -45.685332865
2021-05-17 22:37:13,685 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S400A1
2021-05-17 22:37:13,686 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 2048
2021-05-17 22:37:13,686 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 984 1049
2021-05-17 22:37:13,893 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:37:13,902 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.187759056 -45.682331806 156.186793281 -45.681401531 156.186663358 -45.681468621 156.187629101 -45.682398919
2021-05-17 22:37:13,902 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.187759056 -45.682331806 156.186793281 -45.681401531 156.186663358 -45.681468621 156.187629101 -45.682398919
2021-05-17 22:37:14,227 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S1600A1
2021-05-17 22:37:14,228 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 2048
2021-05-17 22:37:14,229 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 964 1006
2021-05-17 22:37:14,400 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:37:14,408 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.187720636 -45.680802803 156.187307671 -45.680405209 156.186792650 -45.680671077 156.187205560 -45.681068709
2021-05-17 22:37:14,408 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.187720636 -45.680802803 156.187307671 -45.680405209 156.186792650 -45.680671077 156.187205560 -45.681068709
2021-05-17 22:37:14,568 - stpipe.Extract2dStep - INFO - Name of subarray extracted: S200B1
2021-05-17 22:37:14,569 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 140 2048
2021-05-17 22:37:14,569 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 925 1037
2021-05-17 22:37:14,846 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:37:14,855 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.238745821 -45.653926065 156.237887188 -45.653118339 156.237822146 -45.653151380 156.238680762 -45.653959111
2021-05-17 22:37:14,855 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.238745821 -45.653926065 156.237887188 -45.653118339 156.237822146 -45.653151380 156.238680762 -45.653959111
2021-05-17 22:37:15,008 - stpipe.Extract2dStep - INFO - Step Extract2dStep done
2021-05-17 22:37:15,121 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 22:37:15,286 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<MultiSlitModel from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:37:15,288 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:37:15,295 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_FIXEDSLIT
2021-05-17 22:37:15,296 - stpipe.SourceTypeStep - INFO - Input SRCTYAPT = UNKNOWN
2021-05-17 22:37:15,297 - stpipe.SourceTypeStep - INFO - Input source type is unknown; setting default SRCTYPE = POINT
2021-05-17 22:37:15,300 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 22:37:15,317 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 22:37:15,454 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<MultiSlitModel from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:37:15,456 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:37:15,481 - stpipe.WavecorrStep - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0001.asdf
2021-05-17 22:37:16,075 - stpipe.WavecorrStep - INFO - Detected a POINT source type in slit S200A1
2021-05-17 22:37:16,077 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:37:16,339 - stpipe.WavecorrStep - INFO - Using wavelength zero-point correction for aperture S200A1
2021-05-17 22:37:16,351 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 22:37:16,368 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 22:37:16,541 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<MultiSlitModel from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:37:16,543 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 22:37:19,542 - stpipe.FlatFieldStep - INFO - Working on slit S200A1
2021-05-17 22:37:19,544 - stpipe.FlatFieldStep - INFO - Creating wavelength array from WCS for slit S200A1
2021-05-17 22:37:52,267 - stpipe.FlatFieldStep - INFO - Working on slit S200A2
2021-05-17 22:38:08,425 - stpipe.FlatFieldStep - INFO - Working on slit S400A1
2021-05-17 22:38:25,961 - stpipe.FlatFieldStep - INFO - Working on slit S1600A1
2021-05-17 22:38:34,052 - stpipe.FlatFieldStep - INFO - Working on slit S200B1
2021-05-17 22:38:49,707 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 22:38:49,724 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 22:38:49,918 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<MultiSlitModel from fs_fullframe_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 22:38:49,920 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 22:38:49,950 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0001.fits
2021-05-17 22:38:50,019 - stpipe.PathLossStep - INFO - Input exposure type is NRS_FIXEDSLIT
2021-05-17 22:38:50,632 - stpipe.PathLossStep - INFO - Working on slit S200A1
2021-05-17 22:38:50,634 - stpipe.PathLossStep - INFO - Using aperture S200A1
2021-05-17 22:38:50,659 - stpipe.PathLossStep - INFO - Working on slit S200A2
2021-05-17 22:38:50,660 - stpipe.PathLossStep - INFO - Using aperture S200A2
2021-05-17 22:38:50,683 - stpipe.PathLossStep - INFO - Working on slit S400A1
2021-05-17 22:38:50,684 - stpipe.PathLossStep - WARNING - Cannot find matching pathloss model for S400A1
2021-05-17 22:38:50,685 - stpipe.PathLossStep - WARNING - Skipping pathloss correction for this slit
2021-05-17 22:38:50,685 - stpipe.PathLossStep - WARNING - No correction provided for slit 2. Skipping
2021-05-17 22:38:50,686 - stpipe.PathLossStep - INFO - Working on slit S1600A1
2021-05-17 22:38:50,686 - stpipe.PathLossStep - INFO - Using aperture S1600A1
2021-05-17 22:38:50,709 - stpipe.PathLossStep - INFO - Working on slit S200B1
2021-05-17 22:38:50,710 - stpipe.PathLossStep - INFO - Using aperture S200B1
2021-05-17 22:38:50,742 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for FS...
Checking if files exist and obtaining datamodels. This takes a few minutes...
from datamodel --> Detector: NRS2 Grating: G395H Filter: F290LP Lamp: LINE3 EXP_TYPE: NRS_FIXEDSLIT
Now looping through the slits. This may take a while...
Looping through the wavelengths...
Working with slitlet S200A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
Calculating statistics...
Absolute Difference : mean = -4.059e-16 median = -4.441e-16 stdev = 8.382e-17
Maximum AbsoluteDifference = -2.220e-16
Minimum AbsoluteDifference = -4.441e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet S200A2
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_fs_ps.py:304: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/aa0c667e23a747249d9442a76121955c/contents' mode='rb' closefd=True> hdul = fits.open(reffile2use)
<Figure size 432x288 with 0 Axes>
Calculating statistics...
Absolute Difference : mean = -4.060e-16 median = -4.441e-16 stdev = 8.374e-17
Maximum AbsoluteDifference = -2.220e-16
Minimum AbsoluteDifference = -4.441e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet S400A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Unable to retrieve extension.
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
Pipeline pathloss correction in datamodel is empty. Skipping testing this slit.
Working with slitlet S1600A1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
<Figure size 432x288 with 0 Axes>
Calculating statistics...
Absolute Difference : mean = -7.765e-17 median = -2.220e-16 stdev = 1.613e-16
Maximum AbsoluteDifference = 2.220e-16
Minimum AbsoluteDifference = -2.220e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet S200B1
Slitlet name in fits file previous to pathloss
and in pathloss output file are the same.
Retrieved point source extension
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0001.fits
<Figure size 432x288 with 0 Axes>
Calculating statistics...
Absolute Difference : mean = -2.490e-16 median = -2.220e-16 stdev = 1.455e-16
Maximum AbsoluteDifference = 0.000e+00
Minimum AbsoluteDifference = -4.441e-16
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final pathloss test result reported as PASSED ***
('* Script FS_PS.py took ', '3.7904648582140603 minutes to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
Testing files for detector: nrs1
<ipython-input-1-c1525cc413af>:62: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/aa0c667e23a747249d9442a76121955c/contents' mode='rb' closefd=True> median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_fs_ps.pathtest(
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_prism_nrs1_uncal.fits
2021-05-17 22:42:39,395 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:42:39,413 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:42:39,416 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:42:39,418 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:42:39,420 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:42:39,421 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:42:39,423 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:42:39,425 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:42:39,426 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:42:39,430 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:42:39,432 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:42:39,434 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:42:39,436 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:42:39,438 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:42:39,440 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:42:39,443 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:42:39,444 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:42:39,446 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_prism_nrs1_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 22:42:39,888 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_prism_nrs1_uncal.fits',).
2021-05-17 22:42:39,899 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:42:40,030 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_prism_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:42:40,041 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits'.
2021-05-17 22:42:40,043 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2021-05-17 22:42:40,046 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits'.
2021-05-17 22:42:40,048 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2021-05-17 22:42:40,050 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:42:40,051 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2021-05-17 22:42:40,053 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits'.
2021-05-17 22:42:40,056 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:42:40,056 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:42:40,058 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits'.
2021-05-17 22:42:40,060 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits'.
2021-05-17 22:42:40,063 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:42:40,064 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:42:40,065 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:42:40,653 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:42:40,655 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:42:40,840 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:42:40,841 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:42:40,842 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:42:41,191 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:42:41,193 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:42:41,215 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2021-05-17 22:42:41,620 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:42:41,949 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:42:41,951 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:42:41,971 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits
2021-05-17 22:42:42,514 - stpipe.Detector1Pipeline.saturation - INFO - Detected 9869 saturated pixels
2021-05-17 22:42:42,550 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:42:42,576 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:42:42,899 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:42:42,901 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:42:42,902 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:42:42,903 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:42:43,212 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:42:43,214 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:42:43,237 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-05-17 22:42:43,603 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:42:43,928 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:42:43,931 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:42:43,954 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits
2021-05-17 22:42:59,231 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:42:59,642 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:42:59,644 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:42:59,664 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits
2021-05-17 22:43:00,398 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:43:00,552 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:00,554 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:43:00,616 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits
2021-05-17 22:43:04,963 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=4, nframes=1, groupgap=0
2021-05-17 22:43:04,965 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-05-17 22:43:05,457 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:43:06,533 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:06,536 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:43:06,574 - stpipe.Detector1Pipeline.jump - WARNING - Can not apply jump detection when NGROUPS<=4;
2021-05-17 22:43:06,575 - stpipe.Detector1Pipeline.jump - WARNING - Jump step will be skipped
2021-05-17 22:43:06,681 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:43:06,980 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:06,983 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:43:07,141 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-05-17 22:43:07,194 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-05-17 22:43:07,251 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:43:07,252 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2021-05-17 22:43:21,156 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 4
2021-05-17 22:43:21,159 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:1091: RuntimeWarning: divide by zero encountered in true_divide
var_p2 = 1/(s_inv_var_p3.sum(axis=0))
2021-05-17 22:43:21,309 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:43:21,698 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:21,704 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:43:21,777 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:43:21,778 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:43:21,781 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:43:22,148 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:22,151 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:43:22,214 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:43:22,216 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:43:22,219 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:43:22,220 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:43:22,221 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:43:22,232 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:43:22,487 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
MSA shutter configuration file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/V0030006000104_msa.fits
2021-05-17 22:43:22,490 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 22:43:22,637 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-05-17 22:43:22,668 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-05-17 22:43:22,670 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-05-17 22:43:22,671 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-05-17 22:43:22,672 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:43:22,965 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [3, 4]
2021-05-17 22:43:22,966 - stpipe.AssignWcsStep - INFO - Computing WCS for 2 open slitlets
2021-05-17 22:43:22,995 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-05-17 22:43:22,995 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-05-17 22:43:22,996 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-05-17 22:43:22,997 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:43:23,005 - stpipe.AssignWcsStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-05-17 22:43:23,126 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 1
2021-05-17 22:43:23,127 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2021-05-17 22:43:23,128 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 3
2021-05-17 22:43:23,140 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 4
2021-05-17 22:43:23,151 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-05-17 22:43:23,276 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/V0030006000104_msa.fits'}
2021-05-17 22:43:23,487 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 22:43:23,494 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 22:43:23,504 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-05-17 22:43:23,792 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:23,795 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:43:23,814 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-05-17 22:43:23,816 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-05-17 22:43:23,948 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2021-05-17 22:43:23,949 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2021-05-17 22:43:23,950 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2021-05-17 22:43:23,952 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:43:23,961 - stpipe.MSAFlagOpenStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-05-17 22:43:24,087 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-05-17 22:43:24,132 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-05-17 22:43:24,161 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-05-17 22:43:24,244 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-05-17 22:43:24,271 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 22:43:36,482 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-05-17 22:43:36,498 - stpipe.Extract2dStep - INFO - Extract2dStep instance created.
2021-05-17 22:43:37,024 - stpipe.Extract2dStep - INFO - Step Extract2dStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:37,027 - stpipe.Extract2dStep - INFO - Step Extract2dStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'grism_objects': None, 'mmag_extract': 99.0}
2021-05-17 22:43:37,046 - stpipe.Extract2dStep - INFO - EXP_TYPE is NRS_MSASPEC
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/utils.py:72: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
indx = np.asarray(np.floor(np.asarray(value) + 0.5), dtype=np.int)
2021-05-17 22:43:37,223 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 3
2021-05-17 22:43:37,224 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1027 1464
2021-05-17 22:43:37,225 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1971 1983
2021-05-17 22:43:37,358 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:43:37,368 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.216281195 -45.702862740 156.216151591 -45.702738206 156.216089149 -45.702770462 156.216218751 -45.702894998
2021-05-17 22:43:37,369 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.216281195 -45.702862740 156.216151591 -45.702738206 156.216089149 -45.702770462 156.216218751 -45.702894998
2021-05-17 22:43:37,520 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 4
2021-05-17 22:43:37,521 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1275 1699
2021-05-17 22:43:37,521 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 32 43
2021-05-17 22:43:37,647 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:43:37,657 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.168120618 -45.657220874 156.167995139 -45.657100409 156.167933468 -45.657132147 156.168058946 -45.657252613
2021-05-17 22:43:37,658 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.168120618 -45.657220874 156.167995139 -45.657100409 156.167933468 -45.657132147 156.168058946 -45.657252613
2021-05-17 22:43:37,726 - stpipe.Extract2dStep - INFO - Step Extract2dStep done
2021-05-17 22:43:37,754 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 22:43:38,116 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<MultiSlitModel from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:38,119 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:43:38,127 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_MSASPEC
2021-05-17 22:43:38,129 - stpipe.SourceTypeStep - INFO - source_id=3, stellarity=100.0000, type=POINT
2021-05-17 22:43:38,130 - stpipe.SourceTypeStep - INFO - source_id=4, stellarity=100.0000, type=POINT
2021-05-17 22:43:38,131 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 22:43:38,144 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 22:43:38,414 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<MultiSlitModel from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:38,416 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:43:38,440 - stpipe.WavecorrStep - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0002.asdf
2021-05-17 22:43:38,754 - stpipe.WavecorrStep - INFO - Detected a POINT source type in slit 3
2021-05-17 22:43:38,835 - stpipe.WavecorrStep - INFO - Using wavelength zero-point correction for aperture MOS
2021-05-17 22:43:38,839 - stpipe.WavecorrStep - INFO - Detected a POINT source type in slit 4
2021-05-17 22:43:38,905 - stpipe.WavecorrStep - INFO - Using wavelength zero-point correction for aperture MOS
2021-05-17 22:43:38,910 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 22:43:38,926 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 22:43:39,281 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<MultiSlitModel from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:43:39,284 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 22:44:18,892 - stpipe.FlatFieldStep - INFO - Working on slit 3
2021-05-17 22:44:19,558 - stpipe.FlatFieldStep - INFO - Working on slit 4
2021-05-17 22:44:20,259 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 22:44:20,275 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 22:44:20,784 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<MultiSlitModel from mos_prism_nrs1_uncal.fits>,).
2021-05-17 22:44:20,787 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 22:44:20,818 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0002.fits
2021-05-17 22:44:21,024 - stpipe.PathLossStep - INFO - Input exposure type is NRS_MSASPEC
2021-05-17 22:44:21,342 - stpipe.PathLossStep - INFO - Working on slit 0
2021-05-17 22:44:21,359 - stpipe.PathLossStep - INFO - Working on slit 1
2021-05-17 22:44:21,377 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for MOS... Checking if files exist and obtaining datamodels. This takes a few minutes... from datamodel --> Detector: NRS1 Grating: PRISM Filter: CLEAR Lamp: LINE4 EXP_TYPE: NRS_MSASPEC Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0002.fits Looping through the slits... Retrieving reference file extensions Working with slitlet 3 Slitlet name in input file and in pathloss output file are the same. Retrieved point source extension slit_x, slit_y (-0.5, -0.5) Running test for POINT source...
Calculating statistics...
* Unable to calculate statistics because
difference array has all outlier values.
Test will be set to FAILED.
*** Result of the test: FAILED
Working with slitlet 4
Slitlet name in input file and in pathloss output file are the same.
Retrieved point source extension
slit_x, slit_y (-0.5, -0.5)
Running test for POINT source...
Calculating statistics...
* Unable to calculate statistics because
difference array has all outlier values.
Test will be set to FAILED.
*** Result of the test: FAILED
*** Final result for path_loss test will be reported as FAILED ***
('* Script pathloss_mos.py took ', '2.6483089923858643 seconds to finish.')
Did pathloss validation test passed? One or more slits FAILED path_loss test.
Testing files for detector: nrs2
<ipython-input-1-c1525cc413af>:82: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/8e6d6917d5834a76434dc30e12182a4d/contents' mode='rb' closefd=True> median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_mos.pathtest(
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_prism_nrs2_uncal.fits
2021-05-17 22:44:25,066 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:44:25,082 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:44:25,084 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:44:25,085 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:44:25,087 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:44:25,088 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:44:25,090 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:44:25,091 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:44:25,093 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:44:25,094 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:44:25,096 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:44:25,097 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:44:25,099 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:44:25,100 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:44:25,104 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:44:25,106 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:44:25,107 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:44:25,109 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_prism_nrs2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 22:44:25,420 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_prism_nrs2_uncal.fits',).
2021-05-17 22:44:25,432 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:44:25,571 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_prism_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:44:25,581 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0087.fits'.
2021-05-17 22:44:25,583 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits'.
2021-05-17 22:44:25,585 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits'.
2021-05-17 22:44:25,587 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits'.
2021-05-17 22:44:25,589 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:44:25,590 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits'.
2021-05-17 22:44:25,592 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0020.fits'.
2021-05-17 22:44:25,594 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:44:25,595 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:44:25,596 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits'.
2021-05-17 22:44:25,598 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0114.fits'.
2021-05-17 22:44:25,600 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:44:25,600 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:44:25,601 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:44:26,108 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:26,111 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:44:26,255 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:44:26,256 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:44:26,260 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:44:26,507 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:26,509 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:44:26,531 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits
2021-05-17 22:44:26,931 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:44:27,210 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:27,213 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:44:27,234 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits
2021-05-17 22:44:27,705 - stpipe.Detector1Pipeline.saturation - INFO - Detected 5379 saturated pixels
2021-05-17 22:44:27,732 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:44:27,755 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:44:28,006 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:28,009 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:44:28,010 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:44:28,012 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:44:28,215 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:28,217 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:44:28,239 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0114.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-05-17 22:44:28,598 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:44:28,845 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:28,848 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:44:28,871 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0020.fits
2021-05-17 22:44:42,225 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:44:42,635 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:42,637 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:44:42,666 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits
2021-05-17 22:44:43,393 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:44:43,522 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:43,524 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:44:43,585 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0087.fits
2021-05-17 22:44:47,977 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=4, nframes=1, groupgap=0
2021-05-17 22:44:47,979 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-05-17 22:44:48,514 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:44:49,280 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:49,283 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:44:49,315 - stpipe.Detector1Pipeline.jump - WARNING - Can not apply jump detection when NGROUPS<=4;
2021-05-17 22:44:49,316 - stpipe.Detector1Pipeline.jump - WARNING - Jump step will be skipped
2021-05-17 22:44:49,404 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:44:49,525 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:44:49,527 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:44:49,685 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-05-17 22:44:49,736 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-05-17 22:44:49,778 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:44:49,779 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2021-05-17 22:45:01,130 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 4
2021-05-17 22:45:01,134 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:1091: RuntimeWarning: divide by zero encountered in true_divide
var_p2 = 1/(s_inv_var_p3.sum(axis=0))
2021-05-17 22:45:01,268 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:45:01,426 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:45:01,428 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:01,489 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:45:01,491 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:45:01,493 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:45:01,610 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:45:01,612 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:01,672 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:45:01,673 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:45:01,676 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:45:01,678 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:45:01,680 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:45:01,689 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:45:01,811 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs2_uncal.fits>,).
2021-05-17 22:45:01,813 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
MSA shutter configuration file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/V0030006000104_msa.fits
2021-05-17 22:45:01,957 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1 2021-05-17 22:45:01,989 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg 2021-05-17 22:45:01,990 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg 2021-05-17 22:45:01,992 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg 2021-05-17 22:45:01,993 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg 2021-05-17 22:45:02,223 - stpipe.AssignWcsStep - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector. 2021-05-17 22:45:02,268 - stpipe.AssignWcsStep - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector. 2021-05-17 22:45:02,269 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS2: [] 2021-05-17 22:45:02,269 - stpipe.AssignWcsStep - CRITICAL - No open slits fall on detector NRS2.
An error occurred that made the pipeline crash, probably: No open slits fall on detector nrs2 Skipping test for this file. Did pathloss validation test passed? skipped Testing files for detector: nrs1 Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_g140m_line1_NRS1_uncal.fits
2021-05-17 22:45:03,468 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:45:03,482 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:45:03,484 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:45:03,485 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:45:03,488 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:45:03,490 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:45:03,491 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:45:03,493 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:45:03,494 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:45:03,495 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:45:03,497 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:45:03,498 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:45:03,500 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:45:03,501 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:45:03,503 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:45:03,504 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:45:03,506 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:45:03,508 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_g140m_line1_NRS1_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 22:45:03,631 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_g140m_line1_NRS1_uncal.fits',).
2021-05-17 22:45:03,641 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:45:03,763 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_g140m_line1_NRS1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:45:03,772 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits'.
2021-05-17 22:45:03,774 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2021-05-17 22:45:03,777 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0019.fits'.
2021-05-17 22:45:03,779 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits'.
2021-05-17 22:45:03,781 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:45:03,782 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits'.
2021-05-17 22:45:03,784 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2021-05-17 22:45:03,785 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:45:03,786 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:45:03,786 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0023.fits'.
2021-05-17 22:45:03,789 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits'.
2021-05-17 22:45:03,791 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:45:03,791 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:45:03,792 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:45:04,152 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:04,154 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:04,293 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:45:04,294 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:45:04,295 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:45:04,412 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:04,416 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:04,443 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits
2021-05-17 22:45:05,168 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:45:05,287 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:05,289 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:05,308 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0023.fits
2021-05-17 22:45:06,449 - stpipe.Detector1Pipeline.saturation - INFO - Detected 58922 saturated pixels
2021-05-17 22:45:06,470 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:45:06,478 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:45:06,597 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:06,599 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:06,600 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:45:06,601 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:45:06,709 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:06,711 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:06,730 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits
2021-05-17 22:45:09,102 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:45:09,345 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:09,347 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:45:09,356 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2021-05-17 22:45:09,357 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2021-05-17 22:45:09,357 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2021-05-17 22:45:09,358 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.000000
2021-05-17 22:45:09,358 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = True
2021-05-17 22:45:12,013 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:45:12,158 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:12,160 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:12,182 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0019.fits
2021-05-17 22:45:17,108 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:45:17,346 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:17,348 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:45:17,372 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits
2021-05-17 22:45:22,027 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2021-05-17 22:45:22,028 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2021-05-17 22:45:22,294 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:45:22,549 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:22,553 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:45:22,567 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-05-17 22:45:22,580 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-05-17 22:45:22,644 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2021-05-17 22:45:23,571 - stpipe.Detector1Pipeline.jump - INFO - Found 32 possible cores to use for jump detection
2021-05-17 22:45:23,868 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-05-17 22:45:24,141 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-05-17 22:45:25,862 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 64057 pixels with at least one CR
2021-05-17 22:45:28,220 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 4.34949 sec
2021-05-17 22:45:28,225 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 5.657567
2021-05-17 22:45:28,228 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:45:28,527 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:28,529 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:45:28,562 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2021-05-17 22:45:28,612 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-05-17 22:45:28,662 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:45:28,663 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:872: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int,:,:,:] *= ( segs_4[num_int,:,:,:] > 0)
2021-05-17 22:45:55,399 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 6
2021-05-17 22:45:55,401 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-05-17 22:45:55,539 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:45:55,806 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:55,808 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:55,894 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:45:55,895 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:45:55,898 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:45:56,029 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:56,031 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:45:56,107 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:45:56,108 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:45:56,110 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:45:56,111 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:45:56,113 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:45:56,122 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:45:56,259 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:56,261 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
MSA shutter configuration file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/V8460001000101_msa.fits
2021-05-17 22:45:56,429 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-05-17 22:45:56,690 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-05-17 22:45:56,691 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-05-17 22:45:56,692 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-05-17 22:45:56,693 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:45:56,842 - stpipe.AssignWcsStep - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,856 - stpipe.AssignWcsStep - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,869 - stpipe.AssignWcsStep - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,883 - stpipe.AssignWcsStep - INFO - Removing slit 9 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,897 - stpipe.AssignWcsStep - INFO - Removing slit 10 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,910 - stpipe.AssignWcsStep - INFO - Removing slit 11 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,923 - stpipe.AssignWcsStep - INFO - Removing slit 14 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,937 - stpipe.AssignWcsStep - INFO - Removing slit 15 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,951 - stpipe.AssignWcsStep - INFO - Removing slit 16 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,965 - stpipe.AssignWcsStep - INFO - Removing slit 17 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,978 - stpipe.AssignWcsStep - INFO - Removing slit 18 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:56,991 - stpipe.AssignWcsStep - INFO - Removing slit 19 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,004 - stpipe.AssignWcsStep - INFO - Removing slit 21 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,018 - stpipe.AssignWcsStep - INFO - Removing slit 25 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,040 - stpipe.AssignWcsStep - INFO - Removing slit 26 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,054 - stpipe.AssignWcsStep - INFO - Removing slit 27 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,067 - stpipe.AssignWcsStep - INFO - Removing slit 29 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,080 - stpipe.AssignWcsStep - INFO - Removing slit 31 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,094 - stpipe.AssignWcsStep - INFO - Removing slit 32 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,108 - stpipe.AssignWcsStep - INFO - Removing slit 33 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,121 - stpipe.AssignWcsStep - INFO - Removing slit 35 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,139 - stpipe.AssignWcsStep - INFO - Removing slit 37 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,154 - stpipe.AssignWcsStep - INFO - Removing slit 38 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,167 - stpipe.AssignWcsStep - INFO - Removing slit 39 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,181 - stpipe.AssignWcsStep - INFO - Removing slit 41 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,225 - stpipe.AssignWcsStep - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,239 - stpipe.AssignWcsStep - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,252 - stpipe.AssignWcsStep - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,265 - stpipe.AssignWcsStep - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,279 - stpipe.AssignWcsStep - INFO - Removing slit 5 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,324 - stpipe.AssignWcsStep - INFO - Removing slit 12 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,337 - stpipe.AssignWcsStep - INFO - Removing slit 13 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,351 - stpipe.AssignWcsStep - INFO - Removing slit 20 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,364 - stpipe.AssignWcsStep - INFO - Removing slit 22 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,378 - stpipe.AssignWcsStep - INFO - Removing slit 23 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,397 - stpipe.AssignWcsStep - INFO - Removing slit 24 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,410 - stpipe.AssignWcsStep - INFO - Removing slit 28 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,423 - stpipe.AssignWcsStep - INFO - Removing slit 30 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,437 - stpipe.AssignWcsStep - INFO - Removing slit 34 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,450 - stpipe.AssignWcsStep - INFO - Removing slit 36 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,463 - stpipe.AssignWcsStep - INFO - Removing slit 40 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:45:57,780 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]
2021-05-17 22:45:57,781 - stpipe.AssignWcsStep - INFO - Computing WCS for 27 open slitlets
2021-05-17 22:45:57,810 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-05-17 22:45:57,811 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-05-17 22:45:57,812 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-05-17 22:45:57,813 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:45:57,825 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-05-17 22:45:57,947 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 1
2021-05-17 22:45:57,967 - stpipe.AssignWcsStep - INFO - There are 11 open slits in quadrant 2
2021-05-17 22:45:58,079 - stpipe.AssignWcsStep - INFO - There are 4 open slits in quadrant 3
2021-05-17 22:45:58,117 - stpipe.AssignWcsStep - INFO - There are 10 open slits in quadrant 4
2021-05-17 22:45:58,455 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-05-17 22:45:58,614 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/V8460001000101_msa.fits'}
2021-05-17 22:45:59,098 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 22:45:59,107 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 22:45:59,117 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-05-17 22:45:59,288 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:45:59,290 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:45:59,308 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-05-17 22:45:59,310 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-05-17 22:45:59,435 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-05-17 22:45:59,438 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-05-17 22:45:59,439 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-05-17 22:45:59,441 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:45:59,451 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-05-17 22:45:59,574 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-05-17 22:45:59,619 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-05-17 22:45:59,647 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-05-17 22:45:59,729 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-05-17 22:45:59,756 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 22:46:10,959 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-05-17 22:46:10,971 - stpipe.Extract2dStep - INFO - Extract2dStep instance created.
2021-05-17 22:46:11,250 - stpipe.Extract2dStep - INFO - Step Extract2dStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:46:11,253 - stpipe.Extract2dStep - INFO - Step Extract2dStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'grism_objects': None, 'mmag_extract': 99.0}
2021-05-17 22:46:11,276 - stpipe.Extract2dStep - INFO - EXP_TYPE is NRS_MSASPEC
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/utils.py:72: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
indx = np.asarray(np.floor(np.asarray(value) + 0.5), dtype=np.int)
2021-05-17 22:46:11,747 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 53
2021-05-17 22:46:11,748 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1542 2048
2021-05-17 22:46:11,749 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1315 1329
2021-05-17 22:46:11,912 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:11,924 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.226123221 -45.673642180 156.225994086 -45.673519691 156.225931834 -45.673551545 156.226060967 -45.673674035
2021-05-17 22:46:11,925 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.226123221 -45.673642180 156.225994086 -45.673519691 156.225931834 -45.673551545 156.226060967 -45.673674035
2021-05-17 22:46:12,585 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 54
2021-05-17 22:46:12,586 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1542 2048
2021-05-17 22:46:12,587 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1305 1319
2021-05-17 22:46:12,706 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:12,716 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.225872406 -45.673404272 156.225743296 -45.673281804 156.225681049 -45.673313656 156.225810156 -45.673436124
2021-05-17 22:46:12,717 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.225872406 -45.673404272 156.225743296 -45.673281804 156.225681049 -45.673313656 156.225810156 -45.673436124
2021-05-17 22:46:13,346 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 42
2021-05-17 22:46:13,348 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 2018 2048
2021-05-17 22:46:13,349 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 545 562
2021-05-17 22:46:13,464 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:13,475 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.223646010 -45.647128995 156.223518121 -45.647008321 156.223456024 -45.647039957 156.223583911 -45.647160632
2021-05-17 22:46:13,476 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.223646010 -45.647128995 156.223518121 -45.647008321 156.223456024 -45.647039957 156.223583911 -45.647160632
2021-05-17 22:46:13,914 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 43
2021-05-17 22:46:13,915 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1970 2048
2021-05-17 22:46:13,916 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 414 430
2021-05-17 22:46:14,233 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:14,244 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.218966486 -45.644829601 156.218838959 -45.644709141 156.218776943 -45.644740759 156.218904467 -45.644861220
2021-05-17 22:46:14,245 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.218966486 -45.644829601 156.218838959 -45.644709141 156.218776943 -45.644740759 156.218904467 -45.644861220
2021-05-17 22:46:14,689 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 44
2021-05-17 22:46:14,690 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1969 2048
2021-05-17 22:46:14,691 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 404 420
2021-05-17 22:46:14,807 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:14,817 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.218718991 -45.644595818 156.218591488 -45.644475376 156.218529475 -45.644506992 156.218656977 -45.644627436
2021-05-17 22:46:14,819 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.218718991 -45.644595818 156.218591488 -45.644475376 156.218529475 -45.644506992 156.218656977 -45.644627436
2021-05-17 22:46:15,442 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 45
2021-05-17 22:46:15,443 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1908 2048
2021-05-17 22:46:15,444 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 530 546
2021-05-17 22:46:15,561 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:15,570 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.219673020 -45.648613077 156.219545303 -45.648492383 156.219483265 -45.648524021 156.219610979 -45.648644716
2021-05-17 22:46:15,571 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.219673020 -45.648613077 156.219545303 -45.648492383 156.219483265 -45.648524021 156.219610979 -45.648644716
2021-05-17 22:46:16,209 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 46
2021-05-17 22:46:16,211 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1882 2048
2021-05-17 22:46:16,211 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 202 218
2021-05-17 22:46:16,327 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:16,337 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.211127421 -45.641279813 156.211000463 -45.641159678 156.210938572 -45.641191268 156.211065527 -45.641311404
2021-05-17 22:46:16,339 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.211127421 -45.641279813 156.211000463 -45.641159678 156.210938572 -45.641191268 156.211065527 -45.641311404
2021-05-17 22:46:16,774 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 47
2021-05-17 22:46:16,775 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1815 2048
2021-05-17 22:46:16,776 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 566 581
2021-05-17 22:46:16,898 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:16,910 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.217456055 -45.651006881 156.217328370 -45.650886079 156.217266356 -45.650917729 156.217394038 -45.651038531
2021-05-17 22:46:16,911 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.217456055 -45.651006881 156.217328370 -45.650886079 156.217266356 -45.650917729 156.217394038 -45.651038531
2021-05-17 22:46:17,586 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 48
2021-05-17 22:46:17,587 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1815 2048
2021-05-17 22:46:17,588 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 561 576
2021-05-17 22:46:17,711 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:17,722 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.217332149 -45.650889654 156.217204477 -45.650768862 156.217142464 -45.650800511 156.217270135 -45.650921304
2021-05-17 22:46:17,724 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.217332149 -45.650889654 156.217204477 -45.650768862 156.217142464 -45.650800511 156.217270135 -45.650921304
2021-05-17 22:46:18,405 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 49
2021-05-17 22:46:18,406 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1791 2048
2021-05-17 22:46:18,407 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 631 646
2021-05-17 22:46:18,523 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:18,534 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.218210913 -45.652969013 156.218083107 -45.652848076 156.218021073 -45.652879740 156.218148877 -45.653000678
2021-05-17 22:46:18,535 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.218210913 -45.652969013 156.218083107 -45.652848076 156.218021073 -45.652879740 156.218148877 -45.653000678
2021-05-17 22:46:18,976 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 50
2021-05-17 22:46:18,978 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1774 2048
2021-05-17 22:46:18,979 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 238 253
2021-05-17 22:46:19,099 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:19,109 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.208399869 -45.643929179 156.208272959 -45.643808942 156.208211096 -45.643840541 156.208338005 -45.643960778
2021-05-17 22:46:19,110 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.208399869 -45.643929179 156.208272959 -45.643808942 156.208211096 -45.643840541 156.208338005 -45.643960778
2021-05-17 22:46:19,811 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 51
2021-05-17 22:46:19,813 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1759 2048
2021-05-17 22:46:19,813 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 430 445
2021-05-17 22:46:19,937 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:19,948 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.212403238 -45.648718689 156.212275928 -45.648598111 156.212213993 -45.648629742 156.212341301 -45.648750320
2021-05-17 22:46:19,949 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.212403238 -45.648718689 156.212275928 -45.648598111 156.212213993 -45.648629742 156.212341301 -45.648750320
2021-05-17 22:46:20,624 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 52
2021-05-17 22:46:20,625 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1722 2048
2021-05-17 22:46:20,626 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 803 817
2021-05-17 22:46:20,743 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:20,753 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.219947139 -45.658234585 156.219819020 -45.658113276 156.219756938 -45.658144979 156.219885055 -45.658266289
2021-05-17 22:46:20,754 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.219947139 -45.658234585 156.219819020 -45.658113276 156.219756938 -45.658144979 156.219885055 -45.658266289
2021-05-17 22:46:21,221 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 55
2021-05-17 22:46:21,222 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1022 2048
2021-05-17 22:46:21,223 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1415 1430
2021-05-17 22:46:21,351 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:21,361 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.211226719 -45.684941334 156.211098073 -45.684818233 156.211035880 -45.684850241 156.211164524 -45.684973343
2021-05-17 22:46:21,362 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.211226719 -45.684941334 156.211098073 -45.684818233 156.211035880 -45.684850241 156.211164524 -45.684973343
2021-05-17 22:46:22,064 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 65
2021-05-17 22:46:22,069 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 427 1893
2021-05-17 22:46:22,069 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1251 1273
2021-05-17 22:46:22,210 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:22,221 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.187669449 -45.691221095 156.187541886 -45.691097893 156.187479754 -45.691130071 156.187607315 -45.691253274
2021-05-17 22:46:22,221 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.187669449 -45.691221095 156.187541886 -45.691097893 156.187479754 -45.691130071 156.187607315 -45.691253274
2021-05-17 22:46:22,668 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 66
2021-05-17 22:46:22,670 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 426 1892
2021-05-17 22:46:22,670 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1452 1474
2021-05-17 22:46:22,807 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:22,816 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.192290190 -45.696194513 156.192162195 -45.696070854 156.192099979 -45.696103094 156.192227972 -45.696226755
2021-05-17 22:46:22,817 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.192290190 -45.696194513 156.192162195 -45.696070854 156.192099979 -45.696103094 156.192227972 -45.696226755
2021-05-17 22:46:23,538 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 68
2021-05-17 22:46:23,539 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 375 1842
2021-05-17 22:46:23,540 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1476 1499
2021-05-17 22:46:23,677 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:23,685 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.191192483 -45.697686513 156.191064493 -45.697562756 156.191002259 -45.697595026 156.191130247 -45.697718784
2021-05-17 22:46:23,686 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.191192483 -45.697686513 156.191064493 -45.697562756 156.191002259 -45.697595026 156.191130247 -45.697718784
2021-05-17 22:46:24,125 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 56
2021-05-17 22:46:24,126 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 872 2048
2021-05-17 22:46:24,127 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 768 783
2021-05-17 22:46:24,508 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:24,518 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.191122501 -45.671742959 156.190995485 -45.671621176 156.190933579 -45.671653049 156.191060593 -45.671774833
2021-05-17 22:46:24,519 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.191122501 -45.671742959 156.190995485 -45.671621176 156.190933579 -45.671653049 156.191060593 -45.671774833
2021-05-17 22:46:25,004 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 57
2021-05-17 22:46:25,006 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 805 2048
2021-05-17 22:46:25,007 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 354 370
2021-05-17 22:46:25,149 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:25,159 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.179343124 -45.662963603 156.179216994 -45.662842617 156.179155236 -45.662874401 156.179281365 -45.662995389
2021-05-17 22:46:25,159 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.179343124 -45.662963603 156.179216994 -45.662842617 156.179155236 -45.662874401 156.179281365 -45.662995389
2021-05-17 22:46:26,154 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 58
2021-05-17 22:46:26,156 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 731 2048
2021-05-17 22:46:26,156 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 258 274
2021-05-17 22:46:26,295 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:26,306 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.174716949 -45.661919476 156.174591057 -45.661798624 156.174529324 -45.661830406 156.174655215 -45.661951259
2021-05-17 22:46:26,307 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.174716949 -45.661919476 156.174591057 -45.661798624 156.174529324 -45.661830406 156.174655215 -45.661951259
2021-05-17 22:46:26,794 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 59
2021-05-17 22:46:26,796 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 658 2048
2021-05-17 22:46:26,797 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 71 88
2021-05-17 22:46:26,934 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:26,944 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.167987333 -45.658726530 156.167861814 -45.658605973 156.167800128 -45.658637729 156.167925645 -45.658758288
2021-05-17 22:46:26,945 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.167987333 -45.658726530 156.167861814 -45.658605973 156.167800128 -45.658637729 156.167925645 -45.658758288
2021-05-17 22:46:28,009 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 60
2021-05-17 22:46:28,011 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 641 2048
2021-05-17 22:46:28,011 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 681 699
2021-05-17 22:46:28,154 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:28,164 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.181507045 -45.673611447 156.181380443 -45.673489678 156.181318559 -45.673521602 156.181445158 -45.673643373
2021-05-17 22:46:28,165 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.181507045 -45.673611447 156.181380443 -45.673489678 156.181318559 -45.673521602 156.181445158 -45.673643373
2021-05-17 22:46:28,649 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 61
2021-05-17 22:46:28,650 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 620 2048
2021-05-17 22:46:28,650 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 822 840
2021-05-17 22:46:28,787 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:28,797 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.184095390 -45.677365774 156.183968526 -45.677243686 156.183906587 -45.677275659 156.184033450 -45.677397747
2021-05-17 22:46:28,798 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.184095390 -45.677365774 156.183968526 -45.677243686 156.183906587 -45.677275659 156.184033450 -45.677397747
2021-05-17 22:46:29,844 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 62
2021-05-17 22:46:29,845 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 570 2032
2021-05-17 22:46:29,846 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 510 528
2021-05-17 22:46:29,983 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:29,994 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.175200333 -45.670700849 156.175074128 -45.670579384 156.175012293 -45.670611285 156.175138497 -45.670732752
2021-05-17 22:46:29,995 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.175200333 -45.670700849 156.175074128 -45.670579384 156.175012293 -45.670611285 156.175138497 -45.670732752
2021-05-17 22:46:30,471 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 63
2021-05-17 22:46:30,473 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 454 1915
2021-05-17 22:46:30,474 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 181 200
2021-05-17 22:46:30,611 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:30,621 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.163846800 -45.664818400 156.163721256 -45.664697497 156.163659498 -45.664729348 156.163785040 -45.664850252
2021-05-17 22:46:30,622 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.163846800 -45.664818400 156.163721256 -45.664697497 156.163659498 -45.664729348 156.163785040 -45.664850252
2021-05-17 22:46:31,637 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 64
2021-05-17 22:46:31,639 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 454 1915
2021-05-17 22:46:31,640 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 176 195
2021-05-17 22:46:31,777 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:31,791 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.163724974 -45.664701077 156.163599439 -45.664580184 156.163537682 -45.664612033 156.163663216 -45.664732928
2021-05-17 22:46:31,792 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.163724974 -45.664701077 156.163599439 -45.664580184 156.163537682 -45.664612033 156.163663216 -45.664732928
2021-05-17 22:46:32,275 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 67
2021-05-17 22:46:32,278 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 328 1789
2021-05-17 22:46:32,279 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 130 150
2021-05-17 22:46:32,529 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:46:32,541 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.158533940 -45.665758025 156.158408563 -45.665637125 156.158346784 -45.665669007 156.158472159 -45.665789909
2021-05-17 22:46:32,542 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.158533940 -45.665758025 156.158408563 -45.665637125 156.158346784 -45.665669007 156.158472159 -45.665789909
2021-05-17 22:46:33,850 - stpipe.Extract2dStep - INFO - Step Extract2dStep done
2021-05-17 22:46:36,144 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 22:46:36,478 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:46:36,481 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:46:36,489 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_MSASPEC
2021-05-17 22:46:36,491 - stpipe.SourceTypeStep - INFO - source_id=53, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,492 - stpipe.SourceTypeStep - INFO - source_id=54, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,494 - stpipe.SourceTypeStep - INFO - source_id=42, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,495 - stpipe.SourceTypeStep - INFO - source_id=43, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,496 - stpipe.SourceTypeStep - INFO - source_id=44, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,497 - stpipe.SourceTypeStep - INFO - source_id=45, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,498 - stpipe.SourceTypeStep - INFO - source_id=46, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,499 - stpipe.SourceTypeStep - INFO - source_id=47, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,500 - stpipe.SourceTypeStep - INFO - source_id=48, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,501 - stpipe.SourceTypeStep - INFO - source_id=49, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,502 - stpipe.SourceTypeStep - INFO - source_id=50, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,503 - stpipe.SourceTypeStep - INFO - source_id=51, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,505 - stpipe.SourceTypeStep - INFO - source_id=52, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,506 - stpipe.SourceTypeStep - INFO - source_id=55, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,507 - stpipe.SourceTypeStep - INFO - source_id=65, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,508 - stpipe.SourceTypeStep - INFO - source_id=66, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,509 - stpipe.SourceTypeStep - INFO - source_id=68, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,510 - stpipe.SourceTypeStep - INFO - source_id=56, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,511 - stpipe.SourceTypeStep - INFO - source_id=57, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,512 - stpipe.SourceTypeStep - INFO - source_id=58, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,513 - stpipe.SourceTypeStep - INFO - source_id=59, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,514 - stpipe.SourceTypeStep - INFO - source_id=60, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,515 - stpipe.SourceTypeStep - INFO - source_id=61, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,517 - stpipe.SourceTypeStep - INFO - source_id=62, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,518 - stpipe.SourceTypeStep - INFO - source_id=63, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,519 - stpipe.SourceTypeStep - INFO - source_id=64, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,520 - stpipe.SourceTypeStep - INFO - source_id=67, stellarity=0.0000, type=EXTENDED
2021-05-17 22:46:36,521 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 22:46:36,593 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 22:46:36,826 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:46:36,828 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:46:36,892 - stpipe.WavecorrStep - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0002.asdf
2021-05-17 22:46:40,623 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 53
2021-05-17 22:46:40,626 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 54
2021-05-17 22:46:40,627 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 42
2021-05-17 22:46:40,628 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 43
2021-05-17 22:46:40,628 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 44
2021-05-17 22:46:40,629 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 45
2021-05-17 22:46:40,630 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 46
2021-05-17 22:46:40,631 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 47
2021-05-17 22:46:40,631 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 48
2021-05-17 22:46:40,632 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 49
2021-05-17 22:46:40,633 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 50
2021-05-17 22:46:40,634 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 51
2021-05-17 22:46:40,635 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 52
2021-05-17 22:46:40,635 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 55
2021-05-17 22:46:40,636 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 65
2021-05-17 22:46:40,636 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 66
2021-05-17 22:46:40,637 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 68
2021-05-17 22:46:40,638 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 56
2021-05-17 22:46:40,638 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 57
2021-05-17 22:46:40,639 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 58
2021-05-17 22:46:40,639 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 59
2021-05-17 22:46:40,640 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 60
2021-05-17 22:46:40,640 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 61
2021-05-17 22:46:40,641 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 62
2021-05-17 22:46:40,642 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 63
2021-05-17 22:46:40,642 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 64
2021-05-17 22:46:40,643 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 67
2021-05-17 22:46:40,646 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 22:46:40,702 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 22:46:41,109 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:46:41,112 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 22:47:10,623 - stpipe.FlatFieldStep - INFO - Working on slit 53
2021-05-17 22:47:11,401 - stpipe.FlatFieldStep - INFO - Working on slit 54
2021-05-17 22:47:12,144 - stpipe.FlatFieldStep - INFO - Working on slit 42
2021-05-17 22:47:12,274 - stpipe.FlatFieldStep - INFO - Working on slit 43
2021-05-17 22:47:12,461 - stpipe.FlatFieldStep - INFO - Working on slit 44
2021-05-17 22:47:12,647 - stpipe.FlatFieldStep - INFO - Working on slit 45
2021-05-17 22:47:12,931 - stpipe.FlatFieldStep - INFO - Working on slit 46
2021-05-17 22:47:13,267 - stpipe.FlatFieldStep - INFO - Working on slit 47
2021-05-17 22:47:13,648 - stpipe.FlatFieldStep - INFO - Working on slit 48
2021-05-17 22:47:14,023 - stpipe.FlatFieldStep - INFO - Working on slit 49
2021-05-17 22:47:14,442 - stpipe.FlatFieldStep - INFO - Working on slit 50
2021-05-17 22:47:14,885 - stpipe.FlatFieldStep - INFO - Working on slit 51
2021-05-17 22:47:15,336 - stpipe.FlatFieldStep - INFO - Working on slit 52
2021-05-17 22:47:15,833 - stpipe.FlatFieldStep - INFO - Working on slit 55
2021-05-17 22:47:17,236 - stpipe.FlatFieldStep - INFO - Working on slit 65
2021-05-17 22:47:19,248 - stpipe.FlatFieldStep - INFO - Working on slit 66
2021-05-17 22:47:21,263 - stpipe.FlatFieldStep - INFO - Working on slit 68
2021-05-17 22:47:23,308 - stpipe.FlatFieldStep - INFO - Working on slit 56
2021-05-17 22:47:24,916 - stpipe.FlatFieldStep - INFO - Working on slit 57
2021-05-17 22:47:26,670 - stpipe.FlatFieldStep - INFO - Working on slit 58
2021-05-17 22:47:28,362 - stpipe.FlatFieldStep - INFO - Working on slit 59
2021-05-17 22:47:30,255 - stpipe.FlatFieldStep - INFO - Working on slit 60
2021-05-17 22:47:32,188 - stpipe.FlatFieldStep - INFO - Working on slit 61
2021-05-17 22:47:34,049 - stpipe.FlatFieldStep - INFO - Working on slit 62
2021-05-17 22:47:35,956 - stpipe.FlatFieldStep - INFO - Working on slit 63
2021-05-17 22:47:38,035 - stpipe.FlatFieldStep - INFO - Working on slit 64
2021-05-17 22:47:40,824 - stpipe.FlatFieldStep - INFO - Working on slit 67
2021-05-17 22:47:43,726 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 22:47:43,783 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 22:47:44,517 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2021-05-17 22:47:44,520 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 22:47:44,590 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0002.fits
2021-05-17 22:47:44,628 - stpipe.PathLossStep - INFO - Input exposure type is NRS_MSASPEC
2021-05-17 22:47:48,464 - stpipe.PathLossStep - INFO - Working on slit 0
2021-05-17 22:47:48,483 - stpipe.PathLossStep - INFO - Working on slit 1
2021-05-17 22:47:48,498 - stpipe.PathLossStep - INFO - Working on slit 2
2021-05-17 22:47:48,515 - stpipe.PathLossStep - INFO - Working on slit 3
2021-05-17 22:47:48,529 - stpipe.PathLossStep - INFO - Working on slit 4
2021-05-17 22:47:48,546 - stpipe.PathLossStep - INFO - Working on slit 5
2021-05-17 22:47:48,561 - stpipe.PathLossStep - INFO - Working on slit 6
2021-05-17 22:47:48,575 - stpipe.PathLossStep - INFO - Working on slit 7
2021-05-17 22:47:48,590 - stpipe.PathLossStep - INFO - Working on slit 8
2021-05-17 22:47:48,607 - stpipe.PathLossStep - INFO - Working on slit 9
2021-05-17 22:47:48,622 - stpipe.PathLossStep - INFO - Working on slit 10
2021-05-17 22:47:48,637 - stpipe.PathLossStep - INFO - Working on slit 11
2021-05-17 22:47:48,652 - stpipe.PathLossStep - INFO - Working on slit 12
2021-05-17 22:47:48,666 - stpipe.PathLossStep - INFO - Working on slit 13
2021-05-17 22:47:48,683 - stpipe.PathLossStep - INFO - Working on slit 14
2021-05-17 22:47:48,698 - stpipe.PathLossStep - INFO - Working on slit 15
2021-05-17 22:47:48,715 - stpipe.PathLossStep - INFO - Working on slit 16
2021-05-17 22:47:48,731 - stpipe.PathLossStep - INFO - Working on slit 17
2021-05-17 22:47:48,747 - stpipe.PathLossStep - INFO - Working on slit 18
2021-05-17 22:47:48,763 - stpipe.PathLossStep - INFO - Working on slit 19
2021-05-17 22:47:48,778 - stpipe.PathLossStep - INFO - Working on slit 20
2021-05-17 22:47:48,794 - stpipe.PathLossStep - INFO - Working on slit 21
2021-05-17 22:47:48,812 - stpipe.PathLossStep - INFO - Working on slit 22
2021-05-17 22:47:48,827 - stpipe.PathLossStep - INFO - Working on slit 23
2021-05-17 22:47:48,843 - stpipe.PathLossStep - INFO - Working on slit 24
2021-05-17 22:47:48,860 - stpipe.PathLossStep - INFO - Working on slit 25
2021-05-17 22:47:48,877 - stpipe.PathLossStep - INFO - Working on slit 26
2021-05-17 22:47:48,895 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for MOS... Checking if files exist and obtaining datamodels. This takes a few minutes... from datamodel --> Detector: NRS1 Grating: G140M Filter: F100LP Lamp: LINE1 EXP_TYPE: NRS_MSASPEC Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0002.fits Looping through the slits... Retrieving reference file extensions Working with slitlet 53 Slitlet name in input file and in pathloss output file are the same. Retrieved extended/uniform source extension 3 slit_x, slit_y (-0.5, -0.5) Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 3.047e-08 median = 3.052e-08 stdev = 3.500e-08
Maximum AbsoluteDifference = 1.014e-07
Minimum AbsoluteDifference = -4.276e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 54
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 3.062e-08 median = 3.021e-08 stdev = 3.519e-08
Maximum AbsoluteDifference = 1.017e-07
Minimum AbsoluteDifference = -4.294e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 42
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.010e-08 median = 2.020e-08 stdev = 3.461e-08
Maximum AbsoluteDifference = 8.104e-08
Minimum AbsoluteDifference = -4.209e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 43
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.101e-08 median = 2.201e-08 stdev = 3.457e-08
Maximum AbsoluteDifference = 8.671e-08
Minimum AbsoluteDifference = -4.049e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 44
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.273e-08 median = 2.316e-08 stdev = 3.441e-08
Maximum AbsoluteDifference = 8.906e-08
Minimum AbsoluteDifference = -3.935e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 45
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.310e-08 median = 2.285e-08 stdev = 3.454e-08
Maximum AbsoluteDifference = 8.712e-08
Minimum AbsoluteDifference = -4.240e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 46
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.338e-08 median = 2.435e-08 stdev = 3.498e-08
Maximum AbsoluteDifference = 9.236e-08
Minimum AbsoluteDifference = -4.059e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 47
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.401e-08 median = 2.445e-08 stdev = 3.478e-08
Maximum AbsoluteDifference = 9.073e-08
Minimum AbsoluteDifference = -4.101e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 48
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.434e-08 median = 2.480e-08 stdev = 3.485e-08
Maximum AbsoluteDifference = 9.280e-08
Minimum AbsoluteDifference = -4.149e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 49
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.447e-08 median = 2.531e-08 stdev = 3.443e-08
Maximum AbsoluteDifference = 9.232e-08
Minimum AbsoluteDifference = -4.066e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 50
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.619e-08 median = 2.551e-08 stdev = 3.472e-08
Maximum AbsoluteDifference = 9.211e-08
Minimum AbsoluteDifference = -4.060e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 51
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.551e-08 median = 2.548e-08 stdev = 3.390e-08
Maximum AbsoluteDifference = 9.070e-08
Minimum AbsoluteDifference = -3.983e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 52
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.568e-08 median = 2.608e-08 stdev = 3.471e-08
Maximum AbsoluteDifference = 9.395e-08
Minimum AbsoluteDifference = -4.211e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 55
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.716e-08 median = 2.745e-08 stdev = 3.631e-08
Maximum AbsoluteDifference = 1.076e-07
Minimum AbsoluteDifference = -5.777e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 65
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.923e-08 median = 1.909e-08 stdev = 3.791e-08
Maximum AbsoluteDifference = 1.067e-07
Minimum AbsoluteDifference = -7.844e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 66
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.011e-08 median = 1.947e-08 stdev = 3.792e-08
Maximum AbsoluteDifference = 1.071e-07
Minimum AbsoluteDifference = -8.173e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 68
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.936e-08 median = 1.964e-08 stdev = 3.814e-08
Maximum AbsoluteDifference = 1.076e-07
Minimum AbsoluteDifference = -8.090e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 56
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.424e-08 median = 2.391e-08 stdev = 3.693e-08
Maximum AbsoluteDifference = 1.080e-07
Minimum AbsoluteDifference = -5.845e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 57
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.312e-08 median = 2.315e-08 stdev = 3.688e-08
Maximum AbsoluteDifference = 1.062e-07
Minimum AbsoluteDifference = -5.818e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 58
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.242e-08 median = 2.240e-08 stdev = 3.678e-08
Maximum AbsoluteDifference = 1.072e-07
Minimum AbsoluteDifference = -5.979e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 59
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.181e-08 median = 2.162e-08 stdev = 3.704e-08
Maximum AbsoluteDifference = 1.063e-07
Minimum AbsoluteDifference = -7.136e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 60
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.085e-08 median = 2.106e-08 stdev = 3.723e-08
Maximum AbsoluteDifference = 1.087e-07
Minimum AbsoluteDifference = -7.340e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 61
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.111e-08 median = 2.153e-08 stdev = 3.730e-08
Maximum AbsoluteDifference = 1.076e-07
Minimum AbsoluteDifference = -7.841e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 62
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.994e-08 median = 2.002e-08 stdev = 3.793e-08
Maximum AbsoluteDifference = 1.067e-07
Minimum AbsoluteDifference = -7.998e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 63
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.915e-08 median = 1.914e-08 stdev = 3.780e-08
Maximum AbsoluteDifference = 1.049e-07
Minimum AbsoluteDifference = -7.958e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 64
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.006e-08 median = 2.003e-08 stdev = 3.785e-08
Maximum AbsoluteDifference = 1.073e-07
Minimum AbsoluteDifference = -8.405e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 67
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.988e-08 median = 1.988e-08 stdev = 3.763e-08
Maximum AbsoluteDifference = 1.070e-07
Minimum AbsoluteDifference = -8.163e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final result for path_loss test will be reported as PASSED ***
('* Script pathloss_mos.py took ', '25.057603359222412 seconds to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
Testing files for detector: nrs2
<ipython-input-1-c1525cc413af>:82: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/8e6d6917d5834a76434dc30e12182a4d/contents' mode='rb' closefd=True> median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_mos.pathtest(
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_g140m_line1_NRS2_uncal.fits
2021-05-17 22:48:15,109 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:48:15,126 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:48:15,128 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:48:15,129 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:48:15,130 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:48:15,132 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:48:15,133 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:48:15,134 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:48:15,135 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:48:15,137 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:48:15,138 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:48:15,139 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:48:15,140 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:48:15,142 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:48:15,143 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:48:15,144 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:48:15,146 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:48:15,147 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_g140m_line1_NRS2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 22:48:16,270 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/mos_g140m_line1_NRS2_uncal.fits',).
2021-05-17 22:48:16,281 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:48:16,401 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_g140m_line1_NRS2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:48:16,411 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0143.fits'.
2021-05-17 22:48:16,413 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits'.
2021-05-17 22:48:16,415 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0020.fits'.
2021-05-17 22:48:16,417 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0025.fits'.
2021-05-17 22:48:16,419 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:48:16,420 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits'.
2021-05-17 22:48:16,421 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2021-05-17 22:48:16,422 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:48:16,423 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:48:16,423 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0022.fits'.
2021-05-17 22:48:16,425 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0104.fits'.
2021-05-17 22:48:16,427 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:48:16,428 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:48:16,428 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:48:17,626 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:17,628 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:48:17,756 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:48:17,757 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:48:17,759 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:48:18,681 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:18,683 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:48:18,705 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0025.fits
2021-05-17 22:48:19,031 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:48:19,950 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:19,953 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:48:19,974 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0022.fits
2021-05-17 22:48:21,561 - stpipe.Detector1Pipeline.saturation - INFO - Detected 83201 saturated pixels
2021-05-17 22:48:21,584 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:48:21,593 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:48:22,514 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:22,517 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:48:22,518 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:48:22,519 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:48:23,465 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:23,468 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:48:23,491 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0104.fits
2021-05-17 22:48:23,765 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:48:24,695 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:24,697 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:48:24,706 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2021-05-17 22:48:24,707 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2021-05-17 22:48:24,708 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2021-05-17 22:48:24,708 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.000000
2021-05-17 22:48:24,709 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = True
2021-05-17 22:48:27,241 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:48:28,175 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:28,178 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:48:28,201 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0020.fits
2021-05-17 22:48:34,092 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:48:34,956 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:34,959 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:48:34,982 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0143.fits
2021-05-17 22:48:35,353 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2021-05-17 22:48:35,355 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2021-05-17 22:48:35,822 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:48:36,367 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:36,369 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:48:36,379 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-05-17 22:48:36,391 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-05-17 22:48:36,465 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits
2021-05-17 22:48:36,520 - stpipe.Detector1Pipeline.jump - INFO - Found 32 possible cores to use for jump detection
2021-05-17 22:48:36,780 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-05-17 22:48:37,079 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-05-17 22:48:38,931 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 63824 pixels with at least one CR
2021-05-17 22:48:41,631 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 4.84889 sec
2021-05-17 22:48:41,640 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 5.260861
2021-05-17 22:48:41,644 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:48:42,240 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:48:42,243 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:48:42,278 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits
2021-05-17 22:48:42,339 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-05-17 22:48:42,400 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:48:42,402 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:872: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int,:,:,:] *= ( segs_4[num_int,:,:,:] > 0)
2021-05-17 22:49:07,871 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 6
2021-05-17 22:49:07,873 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-05-17 22:49:07,985 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:49:08,549 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:49:08,551 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:49:08,622 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:49:08,623 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:49:08,626 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:49:09,040 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:49:09,042 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:49:09,104 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:49:09,105 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:49:09,108 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:49:09,110 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:49:09,111 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:49:09,120 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:49:09,537 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
MSA shutter configuration file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/V8460001000101_msa.fits
2021-05-17 22:49:09,539 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 22:49:09,730 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2021-05-17 22:49:09,957 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-05-17 22:49:09,958 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-05-17 22:49:09,959 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-05-17 22:49:09,961 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:49:10,784 - stpipe.AssignWcsStep - INFO - Removing slit 65 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,798 - stpipe.AssignWcsStep - INFO - Removing slit 66 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,812 - stpipe.AssignWcsStep - INFO - Removing slit 68 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,851 - stpipe.AssignWcsStep - INFO - Removing slit 58 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,865 - stpipe.AssignWcsStep - INFO - Removing slit 59 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,879 - stpipe.AssignWcsStep - INFO - Removing slit 60 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,893 - stpipe.AssignWcsStep - INFO - Removing slit 61 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,909 - stpipe.AssignWcsStep - INFO - Removing slit 62 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,923 - stpipe.AssignWcsStep - INFO - Removing slit 63 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,937 - stpipe.AssignWcsStep - INFO - Removing slit 64 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,952 - stpipe.AssignWcsStep - INFO - Removing slit 67 from the list of open slits because the WCS bounding_box is completely outside the detector.
2021-05-17 22:49:10,954 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS2: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]
2021-05-17 22:49:10,954 - stpipe.AssignWcsStep - INFO - Computing WCS for 57 open slitlets
2021-05-17 22:49:10,981 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-05-17 22:49:10,982 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-05-17 22:49:10,983 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-05-17 22:49:10,985 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:49:10,994 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-05-17 22:49:11,125 - stpipe.AssignWcsStep - INFO - There are 27 open slits in quadrant 1
2021-05-17 22:49:11,366 - stpipe.AssignWcsStep - INFO - There are 27 open slits in quadrant 2
2021-05-17 22:49:11,592 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 3
2021-05-17 22:49:11,605 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 4
2021-05-17 22:49:11,623 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2021-05-17 22:49:11,777 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/V8460001000101_msa.fits'}
2021-05-17 22:49:13,148 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 22:49:13,155 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 22:49:13,165 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-05-17 22:49:13,707 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:49:13,710 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:49:13,729 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-05-17 22:49:13,731 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-05-17 22:49:13,852 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2021-05-17 22:49:13,853 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2021-05-17 22:49:13,854 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: 0.0002496099796717191 deg
2021-05-17 22:49:13,855 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:49:13,865 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2021-05-17 22:49:13,986 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-05-17 22:49:14,033 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-05-17 22:49:14,061 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-05-17 22:49:14,139 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-05-17 22:49:14,168 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 22:49:26,355 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-05-17 22:49:26,364 - stpipe.Extract2dStep - INFO - Extract2dStep instance created.
2021-05-17 22:49:27,017 - stpipe.Extract2dStep - INFO - Step Extract2dStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:49:27,021 - stpipe.Extract2dStep - INFO - Step Extract2dStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'grism_objects': None, 'mmag_extract': 99.0}
2021-05-17 22:49:27,051 - stpipe.Extract2dStep - INFO - EXP_TYPE is NRS_MSASPEC
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/utils.py:72: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
indx = np.asarray(np.floor(np.asarray(value) + 0.5), dtype=np.int)
2021-05-17 22:49:27,905 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 6
2021-05-17 22:49:27,907 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 138 1619
2021-05-17 22:49:27,907 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1761 1785
2021-05-17 22:49:28,048 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:28,057 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.263159350 -45.671304678 156.263027991 -45.671181725 156.262965146 -45.671213584 156.263096502 -45.671336538
2021-05-17 22:49:28,058 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.263159350 -45.671304678 156.263027991 -45.671181725 156.262965146 -45.671213584 156.263096502 -45.671336538
2021-05-17 22:49:29,442 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 7
2021-05-17 22:49:29,443 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 138 1619
2021-05-17 22:49:29,444 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1756 1780
2021-05-17 22:49:29,586 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:29,595 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.263031777 -45.671185268 156.262900430 -45.671062325 156.262837587 -45.671094183 156.262968931 -45.671217127
2021-05-17 22:49:29,595 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.263031777 -45.671185268 156.262900430 -45.671062325 156.262837587 -45.671094183 156.262968931 -45.671217127
2021-05-17 22:49:30,442 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 8
2021-05-17 22:49:30,443 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 137 1618
2021-05-17 22:49:30,444 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1806 1830
2021-05-17 22:49:30,585 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:30,594 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.264221225 -45.672423837 156.264089757 -45.672300789 156.264026890 -45.672332658 156.264158355 -45.672455707
2021-05-17 22:49:30,595 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.264221225 -45.672423837 156.264089757 -45.672300789 156.264026890 -45.672332658 156.264158355 -45.672455707
2021-05-17 22:49:31,991 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 9
2021-05-17 22:49:31,992 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 137 1618
2021-05-17 22:49:31,992 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1801 1825
2021-05-17 22:49:32,135 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:32,144 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.264093546 -45.672304335 156.263962090 -45.672181297 156.263899225 -45.672213165 156.264030678 -45.672336204
2021-05-17 22:49:32,144 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.264093546 -45.672304335 156.263962090 -45.672181297 156.263899225 -45.672213165 156.264030678 -45.672336204
2021-05-17 22:49:33,503 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 10
2021-05-17 22:49:33,504 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 137 1618
2021-05-17 22:49:33,504 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1796 1820
2021-05-17 22:49:33,649 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:33,659 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.263965879 -45.672184843 156.263834436 -45.672061816 156.263771574 -45.672093683 156.263903014 -45.672216711
2021-05-17 22:49:33,659 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.263965879 -45.672184843 156.263834436 -45.672061816 156.263771574 -45.672093683 156.263903014 -45.672216711
2021-05-17 22:49:34,522 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 11
2021-05-17 22:49:34,524 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 136 1617
2021-05-17 22:49:34,524 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1836 1860
2021-05-17 22:49:34,664 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:34,672 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.264900700 -45.673185083 156.264769161 -45.673061972 156.264706280 -45.673093849 156.264837816 -45.673216961
2021-05-17 22:49:34,673 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.264900700 -45.673185083 156.264769161 -45.673061972 156.264706280 -45.673093849 156.264837816 -45.673216961
2021-05-17 22:49:36,108 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 14
2021-05-17 22:49:36,109 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 104 1582
2021-05-17 22:49:36,109 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1221 1243
2021-05-17 22:49:36,246 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:36,255 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.249021000 -45.658685479 156.248891047 -45.658563629 156.248828487 -45.658595378 156.248958437 -45.658717230
2021-05-17 22:49:36,256 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.249021000 -45.658685479 156.248891047 -45.658563629 156.248828487 -45.658595378 156.248958437 -45.658717230
2021-05-17 22:49:37,106 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 15
2021-05-17 22:49:37,107 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 122 1604
2021-05-17 22:49:37,108 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1886 1910
2021-05-17 22:49:37,247 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:37,256 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.265657550 -45.674645528 156.265525910 -45.674522304 156.265463012 -45.674554193 156.265594650 -45.674677417
2021-05-17 22:49:37,256 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.265657550 -45.674645528 156.265525910 -45.674522304 156.265463012 -45.674554193 156.265594650 -45.674677417
2021-05-17 22:49:38,689 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 16
2021-05-17 22:49:38,690 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 117 1598
2021-05-17 22:49:38,691 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1821 1845
2021-05-17 22:49:38,829 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:38,838 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.263909649 -45.673134588 156.263778173 -45.673011497 156.263715311 -45.673043371 156.263846784 -45.673166463
2021-05-17 22:49:38,838 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.263909649 -45.673134588 156.263778173 -45.673011497 156.263715311 -45.673043371 156.263846784 -45.673166463
2021-05-17 22:49:39,676 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 17
2021-05-17 22:49:39,678 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 115 1597
2021-05-17 22:49:39,678 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1851 1875
2021-05-17 22:49:39,818 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:39,826 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.264589177 -45.673896098 156.264457630 -45.673772943 156.264394753 -45.673804824 156.264526298 -45.673927980
2021-05-17 22:49:39,827 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.264589177 -45.673896098 156.264457630 -45.673772943 156.264394753 -45.673804824 156.264526298 -45.673927980
2021-05-17 22:49:41,257 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 18
2021-05-17 22:49:41,259 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 115 1597
2021-05-17 22:49:41,259 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1846 1870
2021-05-17 22:49:41,398 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:41,406 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.264461421 -45.673776492 156.264329887 -45.673653347 156.264267013 -45.673685227 156.264398544 -45.673808373
2021-05-17 22:49:41,407 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.264461421 -45.673776492 156.264329887 -45.673653347 156.264267013 -45.673685227 156.264398544 -45.673808373
2021-05-17 22:49:42,250 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 19
2021-05-17 22:49:42,251 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 93 1571
2021-05-17 22:49:42,251 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1336 1358
2021-05-17 22:49:42,388 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:42,397 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.251408362 -45.661673296 156.251278132 -45.661551203 156.251215522 -45.661582975 156.251345749 -45.661705069
2021-05-17 22:49:42,397 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.251408362 -45.661673296 156.251278132 -45.661551203 156.251215522 -45.661582975 156.251345749 -45.661705069
2021-05-17 22:49:43,838 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 21
2021-05-17 22:49:43,840 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 89 1568
2021-05-17 22:49:43,840 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1381 1403
2021-05-17 22:49:43,977 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:43,986 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.252374207 -45.662828704 156.252243867 -45.662706516 156.252181238 -45.662738296 156.252311575 -45.662860485
2021-05-17 22:49:43,986 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.252374207 -45.662828704 156.252243867 -45.662706516 156.252181238 -45.662738296 156.252311575 -45.662860485
2021-05-17 22:49:44,828 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 25
2021-05-17 22:49:44,829 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 70 1547
2021-05-17 22:49:44,829 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1276 1298
2021-05-17 22:49:44,966 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:44,975 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.249200048 -45.660601994 156.249070003 -45.660480012 156.249007436 -45.660511773 156.249137478 -45.660633755
2021-05-17 22:49:44,975 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.249200048 -45.660601994 156.249070003 -45.660480012 156.249007436 -45.660511773 156.249137478 -45.660633755
2021-05-17 22:49:46,407 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 26
2021-05-17 22:49:46,408 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 65 1544
2021-05-17 22:49:46,409 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1562 1584
2021-05-17 22:49:46,545 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:46,553 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.255900113 -45.667634746 156.255769353 -45.667512168 156.255706649 -45.667543987 156.255837406 -45.667666566
2021-05-17 22:49:46,554 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.255900113 -45.667634746 156.255769353 -45.667512168 156.255706649 -45.667543987 156.255837406 -45.667666566
2021-05-17 22:49:48,004 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 27
2021-05-17 22:49:48,005 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 31 1507
2021-05-17 22:49:48,006 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1201 1222
2021-05-17 22:49:48,142 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:48,150 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.246097982 -45.659439921 156.245968181 -45.659318074 156.245905674 -45.659349821 156.246035471 -45.659471670
2021-05-17 22:49:48,151 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.246097982 -45.659439921 156.245968181 -45.659318074 156.245905674 -45.659349821 156.246035471 -45.659471670
2021-05-17 22:49:48,991 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 29
2021-05-17 22:49:48,992 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 22 1503
2021-05-17 22:49:48,993 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1867 1889
2021-05-17 22:49:49,133 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:49,150 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.261846987 -45.675840555 156.261715536 -45.675717309 156.261652705 -45.675749201 156.261784154 -45.675872448
2021-05-17 22:49:49,151 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.261846987 -45.675840555 156.261715536 -45.675717309 156.261652705 -45.675749201 156.261784154 -45.675872448
2021-05-17 22:49:50,606 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 31
2021-05-17 22:49:50,608 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1464
2021-05-17 22:49:50,609 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1367 1388
2021-05-17 22:49:50,745 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:50,754 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.248622769 -45.664184605 156.248492610 -45.664062392 156.248430047 -45.664094174 156.248560203 -45.664216388
2021-05-17 22:49:50,754 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.248622769 -45.664184605 156.248492610 -45.664062392 156.248430047 -45.664094174 156.248560203 -45.664216388
2021-05-17 22:49:51,599 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 32
2021-05-17 22:49:51,600 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1432
2021-05-17 22:49:51,601 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1352 1372
2021-05-17 22:49:51,736 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:51,746 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.247206881 -45.664355302 156.247076805 -45.664233103 156.247014266 -45.664264884 156.247144339 -45.664387085
2021-05-17 22:49:51,747 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.247206881 -45.664355302 156.247076805 -45.664233103 156.247014266 -45.664264884 156.247144339 -45.664387085
2021-05-17 22:49:53,203 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 33
2021-05-17 22:49:53,204 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1418
2021-05-17 22:49:53,205 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1272 1292
2021-05-17 22:49:53,338 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:53,348 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.244841867 -45.662633161 156.244712012 -45.662511121 156.244649520 -45.662542887 156.244779372 -45.662664928
2021-05-17 22:49:53,349 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.244841867 -45.662633161 156.244712012 -45.662511121 156.244649520 -45.662542887 156.244779372 -45.662664928
2021-05-17 22:49:54,199 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 35
2021-05-17 22:49:54,200 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1428
2021-05-17 22:49:54,200 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1722 1743
2021-05-17 22:49:54,344 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:54,353 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.255896650 -45.673517700 156.255765657 -45.673394713 156.255702938 -45.673426578 156.255833929 -45.673549566
2021-05-17 22:49:54,354 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.255896650 -45.673517700 156.255765657 -45.673394713 156.255702938 -45.673426578 156.255833929 -45.673549566
2021-05-17 22:49:55,857 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 37
2021-05-17 22:49:55,858 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1412
2021-05-17 22:49:55,859 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1663 1683
2021-05-17 22:49:55,994 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:56,004 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.253937935 -45.672305027 156.253807112 -45.672182158 156.253744431 -45.672214010 156.253875252 -45.672336880
2021-05-17 22:49:56,005 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.253937935 -45.672305027 156.253807112 -45.672182158 156.253744431 -45.672214010 156.253875252 -45.672336880
2021-05-17 22:49:56,856 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 38
2021-05-17 22:49:56,857 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1404
2021-05-17 22:49:56,857 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1603 1623
2021-05-17 22:49:56,993 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:57,003 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.252241050 -45.670961715 156.252110387 -45.670838969 156.252047741 -45.670870808 156.252178401 -45.670993555
2021-05-17 22:49:57,004 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.252241050 -45.670961715 156.252110387 -45.670838969 156.252047741 -45.670870808 156.252178401 -45.670993555
2021-05-17 22:49:58,482 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 39
2021-05-17 22:49:58,483 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1385
2021-05-17 22:49:58,483 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1242 1262
2021-05-17 22:49:58,619 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:58,628 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.243049984 -45.662448591 156.242920250 -45.662326596 156.242857790 -45.662358358 156.242987521 -45.662480354
2021-05-17 22:49:58,629 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.243049984 -45.662448591 156.242920250 -45.662326596 156.242857790 -45.662358358 156.242987521 -45.662480354
2021-05-17 22:49:59,492 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 41
2021-05-17 22:49:59,493 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1393
2021-05-17 22:49:59,493 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1768 1788
2021-05-17 22:49:59,630 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:49:59,640 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.255829101 -45.675209536 156.255698046 -45.675086431 156.255635323 -45.675118310 156.255766375 -45.675241415
2021-05-17 22:49:59,640 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.255829101 -45.675209536 156.255698046 -45.675086431 156.255635323 -45.675118310 156.255766375 -45.675241415
2021-05-17 22:50:00,503 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 53
2021-05-17 22:50:00,504 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 819
2021-05-17 22:50:00,504 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1315 1329
2021-05-17 22:50:01,302 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:01,312 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.226123221 -45.673642180 156.225994086 -45.673519691 156.225931834 -45.673551545 156.226060967 -45.673674035
2021-05-17 22:50:01,313 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.226123221 -45.673642180 156.225994086 -45.673519691 156.225931834 -45.673551545 156.226060967 -45.673674035
2021-05-17 22:50:02,164 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 54
2021-05-17 22:50:02,165 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 819
2021-05-17 22:50:02,165 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1305 1319
2021-05-17 22:50:02,293 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:02,303 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.225872406 -45.673404272 156.225743296 -45.673281804 156.225681049 -45.673313656 156.225810156 -45.673436124
2021-05-17 22:50:02,304 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.225872406 -45.673404272 156.225743296 -45.673281804 156.225681049 -45.673313656 156.225810156 -45.673436124
2021-05-17 22:50:03,741 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 1
2021-05-17 22:50:03,743 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 118 1591
2021-05-17 22:50:03,743 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 33 52
2021-05-17 22:50:03,879 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:03,889 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.221266819 -45.630196596 156.221139727 -45.630076839 156.221077689 -45.630108429 156.221204778 -45.630228186
2021-05-17 22:50:03,890 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.221266819 -45.630196596 156.221139727 -45.630076839 156.221077689 -45.630108429 156.221204778 -45.630228186
2021-05-17 22:50:04,746 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 2
2021-05-17 22:50:04,747 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 124 1598
2021-05-17 22:50:04,748 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 331 351
2021-05-17 22:50:04,884 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:04,892 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.228476955 -45.637109572 156.228349188 -45.636989367 156.228287022 -45.637020983 156.228414786 -45.637141189
2021-05-17 22:50:04,892 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.228476955 -45.637109572 156.228349188 -45.636989367 156.228287022 -45.637020983 156.228414786 -45.637141189
2021-05-17 22:50:05,733 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 3
2021-05-17 22:50:05,734 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 116 1589
2021-05-17 22:50:05,735 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 54 73
2021-05-17 22:50:05,866 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:05,876 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.221674541 -45.630705151 156.221547408 -45.630585366 156.221485363 -45.630616957 156.221612493 -45.630736743
2021-05-17 22:50:05,876 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.221674541 -45.630705151 156.221547408 -45.630585366 156.221485363 -45.630616957 156.221612493 -45.630736743
2021-05-17 22:50:07,413 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 4
2021-05-17 22:50:07,414 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 111 1584
2021-05-17 22:50:07,415 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 160 179
2021-05-17 22:50:07,549 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:07,559 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.224010549 -45.633278787 156.223883188 -45.633158845 156.223821102 -45.633190445 156.223948460 -45.633310387
2021-05-17 22:50:07,560 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.224010549 -45.633278787 156.223883188 -45.633158845 156.223821102 -45.633190445 156.223948460 -45.633310387
2021-05-17 22:50:08,416 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 5
2021-05-17 22:50:08,417 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 99 1573
2021-05-17 22:50:08,418 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 306 326
2021-05-17 22:50:08,553 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:08,561 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.227084510 -45.636919416 156.226956832 -45.636799245 156.226894691 -45.636830857 156.227022367 -45.636951029
2021-05-17 22:50:08,562 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.227084510 -45.636919416 156.226956832 -45.636799245 156.226894691 -45.636830857 156.227022367 -45.636951029
2021-05-17 22:50:10,033 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 12
2021-05-17 22:50:10,034 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 91 1566
2021-05-17 22:50:10,035 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 483 503
2021-05-17 22:50:10,170 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:10,179 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.230998580 -45.641224458 156.230870498 -45.641103991 156.230808285 -45.641135623 156.230936364 -45.641256090
2021-05-17 22:50:10,179 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.230998580 -45.641224458 156.230870498 -45.641103991 156.230808285 -45.641135623 156.230936364 -45.641256090
2021-05-17 22:50:11,037 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 13
2021-05-17 22:50:11,038 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 80 1553
2021-05-17 22:50:11,039 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 94 113
2021-05-17 22:50:11,183 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:11,192 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.221461889 -45.632246282 156.221334710 -45.632126430 156.221272668 -45.632158022 156.221399846 -45.632277874
2021-05-17 22:50:11,193 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.221461889 -45.632246282 156.221334710 -45.632126430 156.221272668 -45.632158022 156.221399846 -45.632277874
2021-05-17 22:50:12,709 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 20
2021-05-17 22:50:12,710 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 76 1551
2021-05-17 22:50:12,711 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 750 770
2021-05-17 22:50:12,850 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:12,858 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.236828252 -45.647826217 156.236699542 -45.647705266 156.236637217 -45.647736933 156.236765924 -45.647857884
2021-05-17 22:50:12,859 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.236828252 -45.647826217 156.236699542 -45.647705266 156.236637217 -45.647736933 156.236765924 -45.647857884
2021-05-17 22:50:13,698 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 22
2021-05-17 22:50:13,699 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 68 1542
2021-05-17 22:50:13,700 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 644 664
2021-05-17 22:50:13,836 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:13,844 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.234035860 -45.645450737 156.233907420 -45.645329977 156.233845148 -45.645361628 156.233973585 -45.645482389
2021-05-17 22:50:13,845 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.234035860 -45.645450737 156.233907420 -45.645329977 156.233845148 -45.645361628 156.233973585 -45.645482389
2021-05-17 22:50:15,353 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 23
2021-05-17 22:50:15,354 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 52 1525
2021-05-17 22:50:15,355 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 115 133
2021-05-17 22:50:15,494 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:15,505 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.221012951 -45.633191592 156.220885760 -45.633071703 156.220823726 -45.633103294 156.220950915 -45.633223183
2021-05-17 22:50:15,506 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.221012951 -45.633191592 156.220885760 -45.633071703 156.220823726 -45.633103294 156.220950915 -45.633223183
2021-05-17 22:50:16,377 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 24
2021-05-17 22:50:16,378 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 69 1545
2021-05-17 22:50:16,378 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 785 805
2021-05-17 22:50:16,516 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:16,524 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.237444560 -45.648779316 156.237315772 -45.648658296 156.237253434 -45.648689968 156.237382219 -45.648810988
2021-05-17 22:50:16,525 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.237444560 -45.648779316 156.237315772 -45.648658296 156.237253434 -45.648689968 156.237382219 -45.648810988
2021-05-17 22:50:18,074 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 28
2021-05-17 22:50:18,076 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 11 1485
2021-05-17 22:50:18,076 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 660 679
2021-05-17 22:50:18,212 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:18,221 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.232517711 -45.646764241 156.232389309 -45.646643431 156.232327062 -45.646675084 156.232455462 -45.646795894
2021-05-17 22:50:18,222 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.232517711 -45.646764241 156.232389309 -45.646643431 156.232327062 -45.646675084 156.232455462 -45.646795894
2021-05-17 22:50:19,070 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 30
2021-05-17 22:50:19,071 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1457
2021-05-17 22:50:19,072 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 700 719
2021-05-17 22:50:19,205 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:19,215 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.232568977 -45.648183467 156.232440513 -45.648062572 156.232378263 -45.648094230 156.232506725 -45.648215126
2021-05-17 22:50:19,215 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.232568977 -45.648183467 156.232440513 -45.648062572 156.232378263 -45.648094230 156.232506725 -45.648215126
2021-05-17 22:50:20,744 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 34
2021-05-17 22:50:20,746 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1394
2021-05-17 22:50:20,747 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 715 734
2021-05-17 22:50:20,881 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:20,891 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.230879662 -45.649585075 156.230751242 -45.649464125 156.230689019 -45.649495787 156.230817437 -45.649616737
2021-05-17 22:50:20,892 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.230879662 -45.649585075 156.230751242 -45.649464125 156.230689019 -45.649495787 156.230817437 -45.649616737
2021-05-17 22:50:21,758 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 36
2021-05-17 22:50:21,759 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1377
2021-05-17 22:50:21,760 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 449 466
2021-05-17 22:50:21,892 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:21,902 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.224033871 -45.643507774 156.223906106 -45.643387302 156.223844011 -45.643418924 156.223971774 -45.643539396
2021-05-17 22:50:21,902 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.224033871 -45.643507774 156.223906106 -45.643387302 156.223844011 -45.643418924 156.223971774 -45.643539396
2021-05-17 22:50:23,468 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 40
2021-05-17 22:50:23,469 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1343
2021-05-17 22:50:23,470 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 217 234
2021-05-17 22:50:23,606 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:23,616 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.217486084 -45.638574970 156.217358883 -45.638454874 156.217296902 -45.638486467 156.217424102 -45.638606563
2021-05-17 22:50:23,616 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.217486084 -45.638574970 156.217358883 -45.638454874 156.217296902 -45.638486467 156.217424102 -45.638606563
2021-05-17 22:50:24,477 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 42
2021-05-17 22:50:24,478 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1296
2021-05-17 22:50:24,479 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 545 562
2021-05-17 22:50:24,610 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:24,620 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.223646010 -45.647128995 156.223518121 -45.647008321 156.223456024 -45.647039957 156.223583911 -45.647160632
2021-05-17 22:50:24,621 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.223646010 -45.647128995 156.223518121 -45.647008321 156.223456024 -45.647039957 156.223583911 -45.647160632
2021-05-17 22:50:25,492 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 43
2021-05-17 22:50:25,493 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1246
2021-05-17 22:50:25,494 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 414 430
2021-05-17 22:50:26,360 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:26,370 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.218966486 -45.644829601 156.218838959 -45.644709141 156.218776943 -45.644740759 156.218904467 -45.644861220
2021-05-17 22:50:26,371 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.218966486 -45.644829601 156.218838959 -45.644709141 156.218776943 -45.644740759 156.218904467 -45.644861220
2021-05-17 22:50:27,229 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 44
2021-05-17 22:50:27,230 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1246
2021-05-17 22:50:27,231 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 404 420
2021-05-17 22:50:27,370 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:27,380 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.218718991 -45.644595818 156.218591488 -45.644475376 156.218529475 -45.644506992 156.218656977 -45.644627436
2021-05-17 22:50:27,381 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.218718991 -45.644595818 156.218591488 -45.644475376 156.218529475 -45.644506992 156.218656977 -45.644627436
2021-05-17 22:50:28,243 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 45
2021-05-17 22:50:28,244 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1185
2021-05-17 22:50:28,244 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 530 546
2021-05-17 22:50:28,375 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:28,384 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.219673020 -45.648613077 156.219545303 -45.648492383 156.219483265 -45.648524021 156.219610979 -45.648644716
2021-05-17 22:50:28,385 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.219673020 -45.648613077 156.219545303 -45.648492383 156.219483265 -45.648524021 156.219610979 -45.648644716
2021-05-17 22:50:29,941 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 46
2021-05-17 22:50:29,942 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1158
2021-05-17 22:50:29,943 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 202 218
2021-05-17 22:50:30,075 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:30,085 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.211127421 -45.641279813 156.211000463 -45.641159678 156.210938572 -45.641191268 156.211065527 -45.641311404
2021-05-17 22:50:30,086 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.211127421 -45.641279813 156.211000463 -45.641159678 156.210938572 -45.641191268 156.211065527 -45.641311404
2021-05-17 22:50:30,928 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 47
2021-05-17 22:50:30,929 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1091
2021-05-17 22:50:30,930 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 566 581
2021-05-17 22:50:31,058 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:31,068 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.217456055 -45.651006881 156.217328370 -45.650886079 156.217266356 -45.650917729 156.217394038 -45.651038531
2021-05-17 22:50:31,068 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.217456055 -45.651006881 156.217328370 -45.650886079 156.217266356 -45.650917729 156.217394038 -45.651038531
2021-05-17 22:50:32,615 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 48
2021-05-17 22:50:32,616 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1091
2021-05-17 22:50:32,617 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 561 576
2021-05-17 22:50:32,744 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:32,755 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.217332149 -45.650889654 156.217204477 -45.650768862 156.217142464 -45.650800511 156.217270135 -45.650921304
2021-05-17 22:50:32,756 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.217332149 -45.650889654 156.217204477 -45.650768862 156.217142464 -45.650800511 156.217270135 -45.650921304
2021-05-17 22:50:33,605 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 49
2021-05-17 22:50:33,606 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1067
2021-05-17 22:50:33,606 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 632 647
2021-05-17 22:50:33,735 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:33,744 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.218210913 -45.652969013 156.218083107 -45.652848076 156.218021073 -45.652879740 156.218148877 -45.653000678
2021-05-17 22:50:33,745 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.218210913 -45.652969013 156.218083107 -45.652848076 156.218021073 -45.652879740 156.218148877 -45.653000678
2021-05-17 22:50:35,319 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 50
2021-05-17 22:50:35,320 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1048
2021-05-17 22:50:35,321 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 238 253
2021-05-17 22:50:35,452 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:35,462 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.208399869 -45.643929179 156.208272959 -45.643808942 156.208211096 -45.643840541 156.208338005 -45.643960778
2021-05-17 22:50:35,463 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.208399869 -45.643929179 156.208272959 -45.643808942 156.208211096 -45.643840541 156.208338005 -45.643960778
2021-05-17 22:50:36,316 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 51
2021-05-17 22:50:36,317 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 1034
2021-05-17 22:50:36,317 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 430 445
2021-05-17 22:50:36,445 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:36,454 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.212403238 -45.648718689 156.212275928 -45.648598111 156.212213993 -45.648629742 156.212341301 -45.648750320
2021-05-17 22:50:36,455 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.212403238 -45.648718689 156.212275928 -45.648598111 156.212213993 -45.648629742 156.212341301 -45.648750320
2021-05-17 22:50:37,309 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 52
2021-05-17 22:50:37,310 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 998
2021-05-17 22:50:37,310 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 803 817
2021-05-17 22:50:37,438 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:37,448 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.219947139 -45.658234585 156.219819020 -45.658113276 156.219756938 -45.658144979 156.219885055 -45.658266289
2021-05-17 22:50:37,449 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.219947139 -45.658234585 156.219819020 -45.658113276 156.219756938 -45.658144979 156.219885055 -45.658266289
2021-05-17 22:50:39,060 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 55
2021-05-17 22:50:39,061 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 297
2021-05-17 22:50:39,062 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1415 1430
2021-05-17 22:50:39,191 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:39,201 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.211226719 -45.684941334 156.211098073 -45.684818233 156.211035880 -45.684850241 156.211164524 -45.684973343
2021-05-17 22:50:39,202 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.211226719 -45.684941334 156.211098073 -45.684818233 156.211035880 -45.684850241 156.211164524 -45.684973343
2021-05-17 22:50:40,050 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 56
2021-05-17 22:50:40,051 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 143
2021-05-17 22:50:40,051 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 768 783
2021-05-17 22:50:40,173 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:40,183 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.191122501 -45.671742959 156.190995485 -45.671621176 156.190933579 -45.671653049 156.191060593 -45.671774833
2021-05-17 22:50:40,183 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.191122501 -45.671742959 156.190995485 -45.671621176 156.190933579 -45.671653049 156.191060593 -45.671774833
2021-05-17 22:50:41,794 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 57
2021-05-17 22:50:41,795 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 0 74
2021-05-17 22:50:41,796 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 354 370
2021-05-17 22:50:41,917 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2021-05-17 22:50:41,927 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS 156.179343124 -45.662963603 156.179216994 -45.662842617 156.179155236 -45.662874401 156.179281365 -45.662995389
2021-05-17 22:50:41,928 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS 156.179343124 -45.662963603 156.179216994 -45.662842617 156.179155236 -45.662874401 156.179281365 -45.662995389
2021-05-17 22:50:43,861 - stpipe.Extract2dStep - INFO - Step Extract2dStep done
2021-05-17 22:50:46,958 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 22:50:47,704 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<MultiSlitModel from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:50:47,707 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:50:47,715 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_MSASPEC
2021-05-17 22:50:47,716 - stpipe.SourceTypeStep - INFO - source_id=6, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,717 - stpipe.SourceTypeStep - INFO - source_id=7, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,718 - stpipe.SourceTypeStep - INFO - source_id=8, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,719 - stpipe.SourceTypeStep - INFO - source_id=9, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,720 - stpipe.SourceTypeStep - INFO - source_id=10, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,721 - stpipe.SourceTypeStep - INFO - source_id=11, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,722 - stpipe.SourceTypeStep - INFO - source_id=14, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,723 - stpipe.SourceTypeStep - INFO - source_id=15, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,724 - stpipe.SourceTypeStep - INFO - source_id=16, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,725 - stpipe.SourceTypeStep - INFO - source_id=17, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,726 - stpipe.SourceTypeStep - INFO - source_id=18, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,727 - stpipe.SourceTypeStep - INFO - source_id=19, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,727 - stpipe.SourceTypeStep - INFO - source_id=21, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,728 - stpipe.SourceTypeStep - INFO - source_id=25, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,729 - stpipe.SourceTypeStep - INFO - source_id=26, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,730 - stpipe.SourceTypeStep - INFO - source_id=27, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,731 - stpipe.SourceTypeStep - INFO - source_id=29, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,732 - stpipe.SourceTypeStep - INFO - source_id=31, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,733 - stpipe.SourceTypeStep - INFO - source_id=32, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,734 - stpipe.SourceTypeStep - INFO - source_id=33, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,735 - stpipe.SourceTypeStep - INFO - source_id=35, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,735 - stpipe.SourceTypeStep - INFO - source_id=37, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,736 - stpipe.SourceTypeStep - INFO - source_id=38, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,737 - stpipe.SourceTypeStep - INFO - source_id=39, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,738 - stpipe.SourceTypeStep - INFO - source_id=41, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,739 - stpipe.SourceTypeStep - INFO - source_id=53, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,740 - stpipe.SourceTypeStep - INFO - source_id=54, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,741 - stpipe.SourceTypeStep - INFO - source_id=1, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,741 - stpipe.SourceTypeStep - INFO - source_id=2, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,742 - stpipe.SourceTypeStep - INFO - source_id=3, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,743 - stpipe.SourceTypeStep - INFO - source_id=4, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,744 - stpipe.SourceTypeStep - INFO - source_id=5, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,745 - stpipe.SourceTypeStep - INFO - source_id=12, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,745 - stpipe.SourceTypeStep - INFO - source_id=13, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,746 - stpipe.SourceTypeStep - INFO - source_id=20, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,747 - stpipe.SourceTypeStep - INFO - source_id=22, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,748 - stpipe.SourceTypeStep - INFO - source_id=23, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,748 - stpipe.SourceTypeStep - INFO - source_id=24, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,749 - stpipe.SourceTypeStep - INFO - source_id=28, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,750 - stpipe.SourceTypeStep - INFO - source_id=30, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,750 - stpipe.SourceTypeStep - INFO - source_id=34, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,751 - stpipe.SourceTypeStep - INFO - source_id=36, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,752 - stpipe.SourceTypeStep - INFO - source_id=40, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,753 - stpipe.SourceTypeStep - INFO - source_id=42, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,753 - stpipe.SourceTypeStep - INFO - source_id=43, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,758 - stpipe.SourceTypeStep - INFO - source_id=44, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,760 - stpipe.SourceTypeStep - INFO - source_id=45, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,761 - stpipe.SourceTypeStep - INFO - source_id=46, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,761 - stpipe.SourceTypeStep - INFO - source_id=47, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,762 - stpipe.SourceTypeStep - INFO - source_id=48, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,763 - stpipe.SourceTypeStep - INFO - source_id=49, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,763 - stpipe.SourceTypeStep - INFO - source_id=50, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,764 - stpipe.SourceTypeStep - INFO - source_id=51, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,765 - stpipe.SourceTypeStep - INFO - source_id=52, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,766 - stpipe.SourceTypeStep - INFO - source_id=55, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,766 - stpipe.SourceTypeStep - INFO - source_id=56, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,767 - stpipe.SourceTypeStep - INFO - source_id=57, stellarity=0.0000, type=EXTENDED
2021-05-17 22:50:47,774 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 22:50:47,888 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 22:50:48,525 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<MultiSlitModel from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:50:48,527 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:50:48,645 - stpipe.WavecorrStep - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0002.asdf
2021-05-17 22:50:56,700 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 6
2021-05-17 22:50:56,701 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 7
2021-05-17 22:50:56,702 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 8
2021-05-17 22:50:56,702 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 9
2021-05-17 22:50:56,703 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 10
2021-05-17 22:50:56,703 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 11
2021-05-17 22:50:56,704 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 14
2021-05-17 22:50:56,704 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 15
2021-05-17 22:50:56,705 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 16
2021-05-17 22:50:56,705 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 17
2021-05-17 22:50:56,706 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 18
2021-05-17 22:50:56,706 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 19
2021-05-17 22:50:56,707 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 21
2021-05-17 22:50:56,707 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 25
2021-05-17 22:50:56,708 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 26
2021-05-17 22:50:56,708 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 27
2021-05-17 22:50:56,709 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 29
2021-05-17 22:50:56,709 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 31
2021-05-17 22:50:56,710 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 32
2021-05-17 22:50:56,710 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 33
2021-05-17 22:50:56,711 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 35
2021-05-17 22:50:56,711 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 37
2021-05-17 22:50:56,712 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 38
2021-05-17 22:50:56,712 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 39
2021-05-17 22:50:56,713 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 41
2021-05-17 22:50:56,713 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 53
2021-05-17 22:50:56,714 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 54
2021-05-17 22:50:56,714 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 1
2021-05-17 22:50:56,715 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 2
2021-05-17 22:50:56,715 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 3
2021-05-17 22:50:56,716 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 4
2021-05-17 22:50:56,716 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 5
2021-05-17 22:50:56,717 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 12
2021-05-17 22:50:56,717 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 13
2021-05-17 22:50:56,717 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 20
2021-05-17 22:50:56,718 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 22
2021-05-17 22:50:56,718 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 23
2021-05-17 22:50:56,718 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 24
2021-05-17 22:50:56,718 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 28
2021-05-17 22:50:56,719 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 30
2021-05-17 22:50:56,719 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 34
2021-05-17 22:50:56,719 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 36
2021-05-17 22:50:56,720 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 40
2021-05-17 22:50:56,720 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 42
2021-05-17 22:50:56,720 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 43
2021-05-17 22:50:56,721 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 44
2021-05-17 22:50:56,722 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 45
2021-05-17 22:50:56,723 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 46
2021-05-17 22:50:56,723 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 47
2021-05-17 22:50:56,723 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 48
2021-05-17 22:50:56,724 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 49
2021-05-17 22:50:56,724 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 50
2021-05-17 22:50:56,724 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 51
2021-05-17 22:50:56,725 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 52
2021-05-17 22:50:56,725 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 55
2021-05-17 22:50:56,725 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 56
2021-05-17 22:50:56,726 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 57
2021-05-17 22:50:56,728 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 22:50:56,831 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 22:50:57,938 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<MultiSlitModel from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:50:57,944 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 22:51:27,184 - stpipe.FlatFieldStep - INFO - Working on slit 6
2021-05-17 22:51:29,273 - stpipe.FlatFieldStep - INFO - Working on slit 7
2021-05-17 22:51:31,344 - stpipe.FlatFieldStep - INFO - Working on slit 8
2021-05-17 22:51:33,509 - stpipe.FlatFieldStep - INFO - Working on slit 9
2021-05-17 22:51:35,633 - stpipe.FlatFieldStep - INFO - Working on slit 10
2021-05-17 22:51:37,921 - stpipe.FlatFieldStep - INFO - Working on slit 11
2021-05-17 22:51:40,193 - stpipe.FlatFieldStep - INFO - Working on slit 14
2021-05-17 22:51:42,471 - stpipe.FlatFieldStep - INFO - Working on slit 15
2021-05-17 22:51:44,500 - stpipe.FlatFieldStep - INFO - Working on slit 16
2021-05-17 22:51:46,493 - stpipe.FlatFieldStep - INFO - Working on slit 17
2021-05-17 22:51:48,480 - stpipe.FlatFieldStep - INFO - Working on slit 18
2021-05-17 22:51:50,481 - stpipe.FlatFieldStep - INFO - Working on slit 19
2021-05-17 22:51:52,463 - stpipe.FlatFieldStep - INFO - Working on slit 21
2021-05-17 22:51:54,447 - stpipe.FlatFieldStep - INFO - Working on slit 25
2021-05-17 22:51:56,462 - stpipe.FlatFieldStep - INFO - Working on slit 26
2021-05-17 22:51:58,445 - stpipe.FlatFieldStep - INFO - Working on slit 27
2021-05-17 22:52:00,455 - stpipe.FlatFieldStep - INFO - Working on slit 29
2021-05-17 22:52:02,446 - stpipe.FlatFieldStep - INFO - Working on slit 31
2021-05-17 22:52:04,446 - stpipe.FlatFieldStep - INFO - Working on slit 32
2021-05-17 22:52:06,482 - stpipe.FlatFieldStep - INFO - Working on slit 33
2021-05-17 22:52:08,485 - stpipe.FlatFieldStep - INFO - Working on slit 35
2021-05-17 22:52:10,492 - stpipe.FlatFieldStep - INFO - Working on slit 37
2021-05-17 22:52:12,504 - stpipe.FlatFieldStep - INFO - Working on slit 38
2021-05-17 22:52:14,483 - stpipe.FlatFieldStep - INFO - Working on slit 39
2021-05-17 22:52:16,449 - stpipe.FlatFieldStep - INFO - Working on slit 41
2021-05-17 22:52:18,406 - stpipe.FlatFieldStep - INFO - Working on slit 53
2021-05-17 22:52:19,600 - stpipe.FlatFieldStep - INFO - Working on slit 54
2021-05-17 22:52:20,798 - stpipe.FlatFieldStep - INFO - Working on slit 1
2021-05-17 22:52:22,911 - stpipe.FlatFieldStep - INFO - Working on slit 2
2021-05-17 22:52:24,989 - stpipe.FlatFieldStep - INFO - Working on slit 3
2021-05-17 22:52:27,085 - stpipe.FlatFieldStep - INFO - Working on slit 4
2021-05-17 22:52:29,141 - stpipe.FlatFieldStep - INFO - Working on slit 5
2021-05-17 22:52:31,213 - stpipe.FlatFieldStep - INFO - Working on slit 12
2021-05-17 22:52:33,280 - stpipe.FlatFieldStep - INFO - Working on slit 13
2021-05-17 22:52:35,500 - stpipe.FlatFieldStep - INFO - Working on slit 20
2021-05-17 22:52:37,546 - stpipe.FlatFieldStep - INFO - Working on slit 22
2021-05-17 22:52:39,628 - stpipe.FlatFieldStep - INFO - Working on slit 23
2021-05-17 22:52:41,688 - stpipe.FlatFieldStep - INFO - Working on slit 24
2021-05-17 22:52:43,779 - stpipe.FlatFieldStep - INFO - Working on slit 28
2021-05-17 22:52:45,830 - stpipe.FlatFieldStep - INFO - Working on slit 30
2021-05-17 22:52:47,876 - stpipe.FlatFieldStep - INFO - Working on slit 34
2021-05-17 22:52:49,847 - stpipe.FlatFieldStep - INFO - Working on slit 36
2021-05-17 22:52:51,787 - stpipe.FlatFieldStep - INFO - Working on slit 40
2021-05-17 22:52:53,675 - stpipe.FlatFieldStep - INFO - Working on slit 42
2021-05-17 22:52:55,479 - stpipe.FlatFieldStep - INFO - Working on slit 43
2021-05-17 22:52:57,225 - stpipe.FlatFieldStep - INFO - Working on slit 44
2021-05-17 22:52:58,981 - stpipe.FlatFieldStep - INFO - Working on slit 45
2021-05-17 22:53:00,660 - stpipe.FlatFieldStep - INFO - Working on slit 46
2021-05-17 22:53:02,329 - stpipe.FlatFieldStep - INFO - Working on slit 47
2021-05-17 22:53:03,910 - stpipe.FlatFieldStep - INFO - Working on slit 48
2021-05-17 22:53:05,492 - stpipe.FlatFieldStep - INFO - Working on slit 49
2021-05-17 22:53:07,038 - stpipe.FlatFieldStep - INFO - Working on slit 50
2021-05-17 22:53:08,570 - stpipe.FlatFieldStep - INFO - Working on slit 51
2021-05-17 22:53:10,089 - stpipe.FlatFieldStep - INFO - Working on slit 52
2021-05-17 22:53:11,536 - stpipe.FlatFieldStep - INFO - Working on slit 55
2021-05-17 22:53:12,032 - stpipe.FlatFieldStep - INFO - Working on slit 56
2021-05-17 22:53:12,319 - stpipe.FlatFieldStep - INFO - Working on slit 57
2021-05-17 22:53:16,149 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 22:53:16,259 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 22:53:17,879 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<MultiSlitModel from mos_g140m_line1_NRS2_uncal.fits>,).
2021-05-17 22:53:17,885 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 22:53:18,013 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0002.fits
2021-05-17 22:53:18,052 - stpipe.PathLossStep - INFO - Input exposure type is NRS_MSASPEC
2021-05-17 22:53:26,284 - stpipe.PathLossStep - INFO - Working on slit 0
2021-05-17 22:53:26,308 - stpipe.PathLossStep - INFO - Working on slit 1
2021-05-17 22:53:26,325 - stpipe.PathLossStep - INFO - Working on slit 2
2021-05-17 22:53:26,342 - stpipe.PathLossStep - INFO - Working on slit 3
2021-05-17 22:53:26,359 - stpipe.PathLossStep - INFO - Working on slit 4
2021-05-17 22:53:26,377 - stpipe.PathLossStep - INFO - Working on slit 5
2021-05-17 22:53:26,395 - stpipe.PathLossStep - INFO - Working on slit 6
2021-05-17 22:53:26,412 - stpipe.PathLossStep - INFO - Working on slit 7
2021-05-17 22:53:26,428 - stpipe.PathLossStep - INFO - Working on slit 8
2021-05-17 22:53:26,446 - stpipe.PathLossStep - INFO - Working on slit 9
2021-05-17 22:53:26,462 - stpipe.PathLossStep - INFO - Working on slit 10
2021-05-17 22:53:26,479 - stpipe.PathLossStep - INFO - Working on slit 11
2021-05-17 22:53:26,496 - stpipe.PathLossStep - INFO - Working on slit 12
2021-05-17 22:53:26,514 - stpipe.PathLossStep - INFO - Working on slit 13
2021-05-17 22:53:26,530 - stpipe.PathLossStep - INFO - Working on slit 14
2021-05-17 22:53:26,547 - stpipe.PathLossStep - INFO - Working on slit 15
2021-05-17 22:53:26,564 - stpipe.PathLossStep - INFO - Working on slit 16
2021-05-17 22:53:26,582 - stpipe.PathLossStep - INFO - Working on slit 17
2021-05-17 22:53:26,599 - stpipe.PathLossStep - INFO - Working on slit 18
2021-05-17 22:53:26,615 - stpipe.PathLossStep - INFO - Working on slit 19
2021-05-17 22:53:26,631 - stpipe.PathLossStep - INFO - Working on slit 20
2021-05-17 22:53:26,649 - stpipe.PathLossStep - INFO - Working on slit 21
2021-05-17 22:53:26,668 - stpipe.PathLossStep - INFO - Working on slit 22
2021-05-17 22:53:26,687 - stpipe.PathLossStep - INFO - Working on slit 23
2021-05-17 22:53:26,704 - stpipe.PathLossStep - INFO - Working on slit 24
2021-05-17 22:53:26,722 - stpipe.PathLossStep - INFO - Working on slit 25
2021-05-17 22:53:26,737 - stpipe.PathLossStep - INFO - Working on slit 26
2021-05-17 22:53:26,753 - stpipe.PathLossStep - INFO - Working on slit 27
2021-05-17 22:53:26,769 - stpipe.PathLossStep - INFO - Working on slit 28
2021-05-17 22:53:26,787 - stpipe.PathLossStep - INFO - Working on slit 29
2021-05-17 22:53:26,804 - stpipe.PathLossStep - INFO - Working on slit 30
2021-05-17 22:53:26,820 - stpipe.PathLossStep - INFO - Working on slit 31
2021-05-17 22:53:26,836 - stpipe.PathLossStep - INFO - Working on slit 32
2021-05-17 22:53:26,855 - stpipe.PathLossStep - INFO - Working on slit 33
2021-05-17 22:53:26,871 - stpipe.PathLossStep - INFO - Working on slit 34
2021-05-17 22:53:26,888 - stpipe.PathLossStep - INFO - Working on slit 35
2021-05-17 22:53:26,904 - stpipe.PathLossStep - INFO - Working on slit 36
2021-05-17 22:53:26,922 - stpipe.PathLossStep - INFO - Working on slit 37
2021-05-17 22:53:26,938 - stpipe.PathLossStep - INFO - Working on slit 38
2021-05-17 22:53:26,955 - stpipe.PathLossStep - INFO - Working on slit 39
2021-05-17 22:53:26,972 - stpipe.PathLossStep - INFO - Working on slit 40
2021-05-17 22:53:26,990 - stpipe.PathLossStep - INFO - Working on slit 41
2021-05-17 22:53:27,006 - stpipe.PathLossStep - INFO - Working on slit 42
2021-05-17 22:53:27,022 - stpipe.PathLossStep - INFO - Working on slit 43
2021-05-17 22:53:27,038 - stpipe.PathLossStep - INFO - Working on slit 44
2021-05-17 22:53:27,056 - stpipe.PathLossStep - INFO - Working on slit 45
2021-05-17 22:53:27,072 - stpipe.PathLossStep - INFO - Working on slit 46
2021-05-17 22:53:27,088 - stpipe.PathLossStep - INFO - Working on slit 47
2021-05-17 22:53:27,105 - stpipe.PathLossStep - INFO - Working on slit 48
2021-05-17 22:53:28,459 - stpipe.PathLossStep - INFO - Working on slit 49
2021-05-17 22:53:28,477 - stpipe.PathLossStep - INFO - Working on slit 50
2021-05-17 22:53:28,496 - stpipe.PathLossStep - INFO - Working on slit 51
2021-05-17 22:53:28,512 - stpipe.PathLossStep - INFO - Working on slit 52
2021-05-17 22:53:28,529 - stpipe.PathLossStep - INFO - Working on slit 53
2021-05-17 22:53:28,545 - stpipe.PathLossStep - INFO - Working on slit 54
2021-05-17 22:53:28,561 - stpipe.PathLossStep - INFO - Working on slit 55
2021-05-17 22:53:28,577 - stpipe.PathLossStep - INFO - Working on slit 56
2021-05-17 22:53:28,598 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for MOS... Checking if files exist and obtaining datamodels. This takes a few minutes... from datamodel --> Detector: NRS2 Grating: G140M Filter: F100LP Lamp: LINE1 EXP_TYPE: NRS_MSASPEC Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0002.fits Looping through the slits... Retrieving reference file extensions Working with slitlet 6 Slitlet name in input file and in pathloss output file are the same. Retrieved extended/uniform source extension 3 slit_x, slit_y (-0.5, -0.5) Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.864e-08 median = 1.868e-08 stdev = 3.798e-08
Maximum AbsoluteDifference = 1.051e-07
Minimum AbsoluteDifference = -8.242e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 7
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.930e-08 median = 1.877e-08 stdev = 3.833e-08
Maximum AbsoluteDifference = 1.067e-07
Minimum AbsoluteDifference = -8.105e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 8
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.039e-08 median = 2.055e-08 stdev = 3.825e-08
Maximum AbsoluteDifference = 1.074e-07
Minimum AbsoluteDifference = -8.252e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 9
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.969e-08 median = 1.983e-08 stdev = 3.837e-08
Maximum AbsoluteDifference = 1.060e-07
Minimum AbsoluteDifference = -7.835e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 10
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.943e-08 median = 1.968e-08 stdev = 3.850e-08
Maximum AbsoluteDifference = 1.065e-07
Minimum AbsoluteDifference = -8.194e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 11
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.987e-08 median = 1.961e-08 stdev = 3.803e-08
Maximum AbsoluteDifference = 1.064e-07
Minimum AbsoluteDifference = -7.960e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 14
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.919e-08 median = 1.922e-08 stdev = 3.793e-08
Maximum AbsoluteDifference = 1.063e-07
Minimum AbsoluteDifference = -8.219e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 15
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.976e-08 median = 1.978e-08 stdev = 3.794e-08
Maximum AbsoluteDifference = 1.082e-07
Minimum AbsoluteDifference = -8.377e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 16
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.912e-08 median = 1.885e-08 stdev = 3.814e-08
Maximum AbsoluteDifference = 1.056e-07
Minimum AbsoluteDifference = -7.947e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 17
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.983e-08 median = 2.029e-08 stdev = 3.794e-08
Maximum AbsoluteDifference = 1.070e-07
Minimum AbsoluteDifference = -8.325e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 18
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.968e-08 median = 2.006e-08 stdev = 3.772e-08
Maximum AbsoluteDifference = 1.045e-07
Minimum AbsoluteDifference = -8.119e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 19
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.967e-08 median = 1.963e-08 stdev = 3.763e-08
Maximum AbsoluteDifference = 1.061e-07
Minimum AbsoluteDifference = -8.289e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 21
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.963e-08 median = 1.977e-08 stdev = 3.796e-08
Maximum AbsoluteDifference = 1.074e-07
Minimum AbsoluteDifference = -7.760e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 25
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.968e-08 median = 1.977e-08 stdev = 3.816e-08
Maximum AbsoluteDifference = 1.064e-07
Minimum AbsoluteDifference = -8.252e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 26
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.958e-08 median = 1.913e-08 stdev = 3.781e-08
Maximum AbsoluteDifference = 1.065e-07
Minimum AbsoluteDifference = -8.173e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 27
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.016e-08 median = 2.042e-08 stdev = 3.763e-08
Maximum AbsoluteDifference = 1.069e-07
Minimum AbsoluteDifference = -8.184e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 29
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.898e-08 median = 1.877e-08 stdev = 3.801e-08
Maximum AbsoluteDifference = 1.082e-07
Minimum AbsoluteDifference = -7.944e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 31
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.934e-08 median = 1.924e-08 stdev = 3.762e-08
Maximum AbsoluteDifference = 1.067e-07
Minimum AbsoluteDifference = -8.184e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 32
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.954e-08 median = 1.948e-08 stdev = 3.768e-08
Maximum AbsoluteDifference = 1.078e-07
Minimum AbsoluteDifference = -8.221e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 33
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.965e-08 median = 1.983e-08 stdev = 3.776e-08
Maximum AbsoluteDifference = 1.085e-07
Minimum AbsoluteDifference = -7.991e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 35
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.935e-08 median = 1.961e-08 stdev = 3.782e-08
Maximum AbsoluteDifference = 1.068e-07
Minimum AbsoluteDifference = -8.282e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 37
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.872e-08 median = 1.809e-08 stdev = 3.836e-08
Maximum AbsoluteDifference = 1.074e-07
Minimum AbsoluteDifference = -7.982e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 38
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.895e-08 median = 1.870e-08 stdev = 3.766e-08
Maximum AbsoluteDifference = 1.028e-07
Minimum AbsoluteDifference = -8.464e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 39
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.987e-08 median = 2.022e-08 stdev = 3.802e-08
Maximum AbsoluteDifference = 1.057e-07
Minimum AbsoluteDifference = -7.990e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 41
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.915e-08 median = 1.878e-08 stdev = 3.799e-08
Maximum AbsoluteDifference = 1.090e-07
Minimum AbsoluteDifference = -7.717e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 53
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 8.532e-09 median = 8.570e-09 stdev = 3.683e-08
Maximum AbsoluteDifference = 9.006e-08
Minimum AbsoluteDifference = -7.879e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 54
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 7.754e-09 median = 7.366e-09 stdev = 3.643e-08
Maximum AbsoluteDifference = 9.238e-08
Minimum AbsoluteDifference = -8.188e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 1
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.919e-08 median = 1.911e-08 stdev = 3.774e-08
Maximum AbsoluteDifference = 1.049e-07
Minimum AbsoluteDifference = -8.542e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 2
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.941e-08 median = 1.930e-08 stdev = 3.791e-08
Maximum AbsoluteDifference = 1.071e-07
Minimum AbsoluteDifference = -8.190e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 3
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.972e-08 median = 1.931e-08 stdev = 3.772e-08
Maximum AbsoluteDifference = 1.067e-07
Minimum AbsoluteDifference = -8.054e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 4
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 2.010e-08 median = 2.035e-08 stdev = 3.780e-08
Maximum AbsoluteDifference = 1.073e-07
Minimum AbsoluteDifference = -8.235e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 5
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.967e-08 median = 1.990e-08 stdev = 3.784e-08
Maximum AbsoluteDifference = 1.054e-07
Minimum AbsoluteDifference = -8.135e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 12
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.986e-08 median = 2.010e-08 stdev = 3.731e-08
Maximum AbsoluteDifference = 1.077e-07
Minimum AbsoluteDifference = -7.992e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 13
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.988e-08 median = 1.996e-08 stdev = 3.791e-08
Maximum AbsoluteDifference = 1.072e-07
Minimum AbsoluteDifference = -8.357e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 20
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.962e-08 median = 1.923e-08 stdev = 3.785e-08
Maximum AbsoluteDifference = 1.055e-07
Minimum AbsoluteDifference = -8.016e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 22
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.973e-08 median = 1.923e-08 stdev = 3.760e-08
Maximum AbsoluteDifference = 1.070e-07
Minimum AbsoluteDifference = -7.895e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 23
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.980e-08 median = 1.992e-08 stdev = 3.808e-08
Maximum AbsoluteDifference = 1.064e-07
Minimum AbsoluteDifference = -7.892e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 24
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.918e-08 median = 1.920e-08 stdev = 3.793e-08
Maximum AbsoluteDifference = 1.053e-07
Minimum AbsoluteDifference = -8.297e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 28
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.998e-08 median = 2.057e-08 stdev = 3.804e-08
Maximum AbsoluteDifference = 1.077e-07
Minimum AbsoluteDifference = -8.184e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 30
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.947e-08 median = 1.939e-08 stdev = 3.788e-08
Maximum AbsoluteDifference = 1.068e-07
Minimum AbsoluteDifference = -8.446e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 34
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.928e-08 median = 1.924e-08 stdev = 3.803e-08
Maximum AbsoluteDifference = 1.067e-07
Minimum AbsoluteDifference = -8.164e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 36
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.930e-08 median = 1.939e-08 stdev = 3.804e-08
Maximum AbsoluteDifference = 1.070e-07
Minimum AbsoluteDifference = -8.143e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 40
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.929e-08 median = 1.999e-08 stdev = 3.833e-08
Maximum AbsoluteDifference = 1.066e-07
Minimum AbsoluteDifference = -8.363e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 42
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.912e-08 median = 1.919e-08 stdev = 3.795e-08
Maximum AbsoluteDifference = 1.062e-07
Minimum AbsoluteDifference = -8.136e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 43
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.815e-08 median = 1.753e-08 stdev = 3.814e-08
Maximum AbsoluteDifference = 1.081e-07
Minimum AbsoluteDifference = -8.316e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 44
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.961e-08 median = 1.954e-08 stdev = 3.855e-08
Maximum AbsoluteDifference = 1.068e-07
Minimum AbsoluteDifference = -8.130e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 45
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.867e-08 median = 1.939e-08 stdev = 3.812e-08
Maximum AbsoluteDifference = 1.087e-07
Minimum AbsoluteDifference = -8.060e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 46
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.783e-08 median = 1.766e-08 stdev = 3.860e-08
Maximum AbsoluteDifference = 1.065e-07
Minimum AbsoluteDifference = -8.424e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 47
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.732e-08 median = 1.725e-08 stdev = 3.842e-08
Maximum AbsoluteDifference = 1.078e-07
Minimum AbsoluteDifference = -7.880e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 48
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.718e-08 median = 1.751e-08 stdev = 3.835e-08
Maximum AbsoluteDifference = 1.060e-07
Minimum AbsoluteDifference = -8.121e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 49
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.605e-08 median = 1.620e-08 stdev = 3.860e-08
Maximum AbsoluteDifference = 1.074e-07
Minimum AbsoluteDifference = -8.295e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 50
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.606e-08 median = 1.573e-08 stdev = 3.826e-08
Maximum AbsoluteDifference = 1.065e-07
Minimum AbsoluteDifference = -8.010e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 51
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.580e-08 median = 1.529e-08 stdev = 3.817e-08
Maximum AbsoluteDifference = 1.073e-07
Minimum AbsoluteDifference = -8.031e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 52
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = 1.473e-08 median = 1.468e-08 stdev = 3.816e-08
Maximum AbsoluteDifference = 1.077e-07
Minimum AbsoluteDifference = -8.378e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 55
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = -6.242e-11 median = -1.866e-11 stdev = 3.624e-08
Maximum AbsoluteDifference = 7.672e-08
Minimum AbsoluteDifference = -8.259e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 56
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = -1.035e-08 median = -8.834e-09 stdev = 3.519e-08
Maximum AbsoluteDifference = 6.554e-08
Minimum AbsoluteDifference = -7.788e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
Working with slitlet 57
Slitlet name in input file and in pathloss output file are the same.
Retrieved extended/uniform source extension 3
slit_x, slit_y (-0.5, -0.5)
Running test for UNIFORM source...
Calculating statistics...
Absolute Difference : mean = -1.279e-08 median = -1.257e-08 stdev = 3.503e-08
Maximum AbsoluteDifference = 5.573e-08
Minimum AbsoluteDifference = -8.043e-08
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final result for path_loss test will be reported as PASSED ***
('* Script pathloss_mos.py took ', '55.595782995224 seconds to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
Testing files for detector: nrs1
<ipython-input-1-c1525cc413af>:82: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/8e6d6917d5834a76434dc30e12182a4d/contents' mode='rb' closefd=True> median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_mos.pathtest(
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_prism_nrs1_uncal.fits
2021-05-17 22:54:25,805 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 22:54:25,822 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 22:54:25,824 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 22:54:25,826 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 22:54:25,827 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 22:54:25,829 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 22:54:25,830 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 22:54:25,832 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 22:54:25,833 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 22:54:25,835 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 22:54:25,836 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 22:54:25,838 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 22:54:25,839 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 22:54:25,840 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 22:54:25,842 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 22:54:25,843 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 22:54:25,845 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 22:54:25,847 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_prism_nrs1_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 22:54:27,947 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_prism_nrs1_uncal.fits',).
2021-05-17 22:54:27,959 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 22:54:28,104 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_prism_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 22:54:28,114 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits'.
2021-05-17 22:54:28,116 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2021-05-17 22:54:28,119 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits'.
2021-05-17 22:54:28,121 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits'.
2021-05-17 22:54:28,123 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 22:54:28,124 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits'.
2021-05-17 22:54:28,126 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2021-05-17 22:54:28,126 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 22:54:28,127 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 22:54:28,128 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits'.
2021-05-17 22:54:28,130 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits'.
2021-05-17 22:54:28,132 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 22:54:28,133 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 22:54:28,133 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 22:54:30,385 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:30,388 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:54:30,629 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 22:54:30,631 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 22:54:30,632 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 22:54:32,589 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:32,591 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:54:32,616 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits
2021-05-17 22:54:33,071 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 22:54:35,006 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:35,009 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:54:35,030 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits
2021-05-17 22:54:35,647 - stpipe.Detector1Pipeline.saturation - INFO - Detected 4320 saturated pixels
2021-05-17 22:54:35,694 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 22:54:35,704 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 22:54:37,672 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:37,677 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:54:37,678 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 22:54:37,681 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 22:54:38,694 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:38,696 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:54:38,721 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits
2021-05-17 22:54:39,205 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 22:54:40,099 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:40,102 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 22:54:40,111 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2021-05-17 22:54:40,112 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2021-05-17 22:54:40,113 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2021-05-17 22:54:40,114 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.000000
2021-05-17 22:54:40,115 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = True
2021-05-17 22:54:44,297 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 22:54:45,214 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:45,216 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:54:45,237 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits
2021-05-17 22:54:46,540 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 22:54:48,354 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:48,356 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 22:54:48,377 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits
2021-05-17 22:54:48,646 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=10, nframes=1, groupgap=0
2021-05-17 22:54:48,647 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2021-05-17 22:54:49,173 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 22:54:51,142 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:51,144 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 22:54:51,154 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-05-17 22:54:51,167 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-05-17 22:54:51,228 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2021-05-17 22:54:51,271 - stpipe.Detector1Pipeline.jump - INFO - Found 32 possible cores to use for jump detection
2021-05-17 22:54:51,557 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-05-17 22:54:51,956 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-05-17 22:54:54,379 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 37391 pixels with at least one CR
2021-05-17 22:54:55,609 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 4.05068 sec
2021-05-17 22:54:55,612 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 4.458108
2021-05-17 22:54:55,615 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 22:54:57,620 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:54:57,623 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 22:54:57,657 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2021-05-17 22:54:57,710 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2021-05-17 22:54:57,757 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 22:54:57,758 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:872: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int,:,:,:] *= ( segs_4[num_int,:,:,:] > 0)
2021-05-17 22:55:50,301 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 10
2021-05-17 22:55:50,303 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-05-17 22:55:50,501 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 22:55:51,766 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:55:51,769 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:55:51,851 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:55:51,853 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:55:51,856 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:55:52,781 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:55:52,784 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 22:55:52,849 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 22:55:52,850 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 22:55:52,854 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 22:55:52,856 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 22:55:52,858 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 22:55:52,871 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 22:55:53,828 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:55:53,830 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 22:55:54,017 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.03312480077147484 deg
2021-05-17 22:55:54,019 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3411945700645447 deg
2021-05-17 22:55:54,020 - stpipe.AssignWcsStep - INFO - theta_y correction: -0.005294283663966503 deg
2021-05-17 22:55:54,023 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:55:57,964 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 22:57:05,548 - stpipe.AssignWcsStep - INFO - Update S_REGION to POLYGON ICRS 156.176998032 -45.687618307 156.178780407 -45.687618307 156.178780407 -45.686330486 156.176998032 -45.686330486
2021-05-17 22:57:05,549 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 22:57:05,558 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 22:57:05,571 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-05-17 22:57:07,395 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:57:07,405 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:57:07,431 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-05-17 22:57:07,433 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-05-17 22:57:07,575 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.03312480077147484 deg
2021-05-17 22:57:07,576 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3411945700645447 deg
2021-05-17 22:57:07,577 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -0.005294283663966503 deg
2021-05-17 22:57:07,579 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-05-17 22:57:07,594 - stpipe.MSAFlagOpenStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2021-05-17 22:57:07,718 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-05-17 22:57:07,762 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-05-17 22:57:07,791 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-05-17 22:57:07,869 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-05-17 22:57:07,896 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
2021-05-17 22:57:22,142 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-05-17 22:57:22,152 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 22:57:23,359 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:57:23,366 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:57:23,375 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_IFU
2021-05-17 22:57:23,377 - stpipe.SourceTypeStep - INFO - Input SRCTYAPT = UNKNOWN
2021-05-17 22:57:23,377 - stpipe.SourceTypeStep - INFO - Input source type is unknown; setting default SRCTYPE = EXTENDED
2021-05-17 22:57:23,379 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 22:57:23,389 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 22:57:24,207 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:57:24,208 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 22:57:24,217 - stpipe.WavecorrStep - INFO - Skipping wavecorr correction for EXP_TYPE NRS_IFU
2021-05-17 22:57:24,219 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 22:57:24,230 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 22:57:24,998 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 22:57:25,000 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 23:00:16,944 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 23:00:16,959 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 23:00:18,891 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2021-05-17 23:00:18,900 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 23:00:18,928 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0003.fits
2021-05-17 23:00:18,966 - stpipe.PathLossStep - INFO - Input exposure type is NRS_IFU
2021-05-17 23:01:30,833 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for IFU... Checking if files exist and obtaining datamodels. This takes a few minutes... from datamodel --> Detector: NRS1 Grating: PRISM Filter: CLEAR Lamp: NO_LAMP EXP_TYPE: NRS_IFU Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0003.fits got input slices PLCOR_REF.shape (21, 21, 21) Looping through the slices... working with slice 0 SHAPES (41, 439) (40, 438) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V6 final left 779, right 819, top 999, bottom 561 NEW SHAPE OF SLICE: (40, 438) and corr_vals.shape: (40, 438)
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_ifu_uni.py:168: RuntimeWarning: invalid value encountered in true_divide pathloss_divided = comp_sci/previous_sci
working with slice 1 SHAPES (41, 441) (42, 442) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V8 final left 1195, right 1237, top 946, bottom 504 NEW SHAPE OF SLICE: (42, 442) and corr_vals.shape: (42, 442)
working with slice 2 SHAPES (41, 438) (41, 438)
working with slice 3 SHAPES (41, 442) (42, 442) ALTERED SHAPE OF SLICE: V4 final left 1244, right 1286, top 940, bottom 498 NEW SHAPE OF SLICE: (42, 442) and corr_vals.shape: (42, 442)
working with slice 4 SHAPES (41, 437) (41, 438) ALTERED SHAPE OF SLICE: V8 final left 679, right 720, top 1010, bottom 572 NEW SHAPE OF SLICE: (41, 438) and corr_vals.shape: (41, 438)
working with slice 5 SHAPES (42, 442) (42, 442)
working with slice 6 SHAPES (41, 437) (40, 438) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V8 final left 631, right 671, top 1016, bottom 578 NEW SHAPE OF SLICE: (40, 438) and corr_vals.shape: (40, 438)
working with slice 7 SHAPES (42, 443) (41, 443) ALTERED SHAPE OF SLICE: V2 final left 1344, right 1385, top 926, bottom 483 NEW SHAPE OF SLICE: (41, 443) and corr_vals.shape: (41, 443)
working with slice 8 SHAPES (41, 437) (41, 437)
working with slice 9 SHAPES (42, 443) (41, 443) ALTERED SHAPE OF SLICE: V2 final left 1393, right 1434, top 919, bottom 476 NEW SHAPE OF SLICE: (41, 443) and corr_vals.shape: (41, 443)
working with slice 10 SHAPES (41, 436) (41, 437) ALTERED SHAPE OF SLICE: V8 final left 531, right 572, top 1027, bottom 590 NEW SHAPE OF SLICE: (41, 437) and corr_vals.shape: (41, 437)
working with slice 11 SHAPES (42, 443) (42, 444) ALTERED SHAPE OF SLICE: V8 final left 1441, right 1483, top 912, bottom 468 NEW SHAPE OF SLICE: (42, 444) and corr_vals.shape: (42, 444)
working with slice 12 SHAPES (41, 437) (40, 436) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V6 final left 483, right 523, top 1033, bottom 597 NEW SHAPE OF SLICE: (40, 436) and corr_vals.shape: (40, 436)
working with slice 13 SHAPES (42, 443) (42, 444) ALTERED SHAPE OF SLICE: V8 final left 1490, right 1532, top 905, bottom 461 NEW SHAPE OF SLICE: (42, 444) and corr_vals.shape: (42, 444)
working with slice 14 SHAPES (41, 436) (41, 436)
working with slice 15 SHAPES (42, 444) (42, 444)
working with slice 16 SHAPES (41, 436) (41, 436)
working with slice 17 SHAPES (42, 444) (42, 445) ALTERED SHAPE OF SLICE: V8 final left 1588, right 1630, top 891, bottom 446 NEW SHAPE OF SLICE: (42, 445) and corr_vals.shape: (42, 445)
working with slice 18 SHAPES (41, 436) (40, 435) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V6 final left 335, right 375, top 1049, bottom 614 NEW SHAPE OF SLICE: (40, 435) and corr_vals.shape: (40, 435)
working with slice 19 SHAPES (42, 445) (42, 445)
working with slice 20 SHAPES (41, 435) (41, 436) ALTERED SHAPE OF SLICE: V8 final left 285, right 326, top 1054, bottom 618 NEW SHAPE OF SLICE: (41, 436) and corr_vals.shape: (41, 436)
working with slice 21 SHAPES (42, 446) (42, 445) ALTERED SHAPE OF SLICE: V6 final left 1686, right 1728, top 877, bottom 432 NEW SHAPE OF SLICE: (42, 445) and corr_vals.shape: (42, 445)
working with slice 22 SHAPES (41, 435) (41, 435)
working with slice 23 SHAPES (42, 446) (42, 446)
working with slice 24 SHAPES (41, 435) (41, 435)
working with slice 25 SHAPES (42, 446) (43, 447) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V8 final left 1783, right 1826, top 862, bottom 415 NEW SHAPE OF SLICE: (43, 447) and corr_vals.shape: (43, 447)
working with slice 26 SHAPES (41, 435) (41, 435)
working with slice 27 SHAPES (43, 447) (43, 447)
working with slice 28 SHAPES (41, 434) (41, 435) ALTERED SHAPE OF SLICE: V8 final left 87, right 128, top 1074, bottom 639 NEW SHAPE OF SLICE: (41, 435) and corr_vals.shape: (41, 435)
working with slice 29 SHAPES (43, 447) (43, 447)
Calculating statistics...
Absolute Difference : mean = 0.000e+00 median = 0.000e+00 stdev = 0.000e+00
Maximum AbsoluteDifference = 0.000e+00
Minimum AbsoluteDifference = 0.000e+00
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final result of pathloss test is PASSED ***
('* Script ifu_uni.py took ', '1.5141067822774252 minutes to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
Testing files for detector: nrs2
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_prism_nrs2_uncal.fits
2021-05-17 23:03:03,306 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 23:03:03,330 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 23:03:03,332 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 23:03:03,334 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 23:03:03,336 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 23:03:03,338 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 23:03:03,340 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 23:03:03,342 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 23:03:03,343 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 23:03:03,345 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 23:03:03,346 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 23:03:03,348 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 23:03:03,349 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 23:03:03,351 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 23:03:03,354 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 23:03:03,355 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 23:03:03,357 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 23:03:03,362 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_prism_nrs2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 23:03:04,165 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_prism_nrs2_uncal.fits',).
2021-05-17 23:03:04,179 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 23:03:04,319 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_prism_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 23:03:04,328 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0143.fits'.
2021-05-17 23:03:04,331 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits'.
2021-05-17 23:03:04,333 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits'.
2021-05-17 23:03:04,336 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0025.fits'.
2021-05-17 23:03:04,338 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 23:03:04,339 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits'.
2021-05-17 23:03:04,341 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2021-05-17 23:03:04,342 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 23:03:04,343 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 23:03:04,344 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits'.
2021-05-17 23:03:04,346 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0104.fits'.
2021-05-17 23:03:04,348 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 23:03:04,349 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 23:03:04,350 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 23:03:05,145 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:05,148 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:03:05,347 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 23:03:05,348 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 23:03:05,350 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 23:03:05,787 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:05,790 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:03:05,817 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0025.fits
2021-05-17 23:03:06,239 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 23:03:06,667 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:06,669 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:03:06,688 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0021.fits
2021-05-17 23:03:07,368 - stpipe.Detector1Pipeline.saturation - INFO - Detected 2388 saturated pixels
2021-05-17 23:03:07,417 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 23:03:07,426 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 23:03:07,885 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:07,887 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:03:07,888 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 23:03:07,890 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 23:03:08,323 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:08,325 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:03:08,350 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0104.fits
2021-05-17 23:03:08,828 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 23:03:09,261 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:09,263 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 23:03:09,271 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2021-05-17 23:03:09,273 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2021-05-17 23:03:09,273 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2021-05-17 23:03:09,274 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.000000
2021-05-17 23:03:09,275 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = True
2021-05-17 23:03:14,813 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 23:03:15,270 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:15,273 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:03:15,297 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0021.fits
2021-05-17 23:03:16,520 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 23:03:16,966 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:16,968 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 23:03:16,988 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0143.fits
2021-05-17 23:03:17,226 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=10, nframes=1, groupgap=0
2021-05-17 23:03:17,227 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2021-05-17 23:03:17,614 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 23:03:18,075 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:18,077 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 23:03:18,086 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-05-17 23:03:18,100 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-05-17 23:03:18,158 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits
2021-05-17 23:03:18,217 - stpipe.Detector1Pipeline.jump - INFO - Found 32 possible cores to use for jump detection
2021-05-17 23:03:18,520 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-05-17 23:03:18,942 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-05-17 23:03:21,339 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 16206 pixels with at least one CR
2021-05-17 23:03:22,078 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 3.5568 sec
2021-05-17 23:03:22,080 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 3.994338
2021-05-17 23:03:22,084 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 23:03:22,552 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:03:22,554 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 23:03:22,586 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0016.fits
2021-05-17 23:03:22,636 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0018.fits
2021-05-17 23:03:22,683 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 23:03:22,685 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:872: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int,:,:,:] *= ( segs_4[num_int,:,:,:] > 0)
2021-05-17 23:04:04,040 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 10
2021-05-17 23:04:04,041 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-05-17 23:04:04,223 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 23:04:04,703 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:04:04,705 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:04:04,783 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 23:04:04,784 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 23:04:04,787 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 23:04:05,222 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:04:05,224 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:04:05,291 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2021-05-17 23:04:05,292 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2021-05-17 23:04:05,295 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 23:04:05,297 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 23:04:05,298 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 23:04:05,309 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 23:04:05,749 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs2_uncal.fits>,).
2021-05-17 23:04:05,751 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 23:04:05,922 - stpipe.AssignWcsStep - CRITICAL - No IFU slices fall on detector NRS2
An error occurred that made the pipeline crash, probably: No open slits fall on detector nrs2 Skipping test for this file. Did pathloss validation test passed? skipped Testing files for detector: nrs1 Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_g395h_f290lp_nrs1_uncal.fits
2021-05-17 23:04:10,470 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 23:04:10,486 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 23:04:10,488 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 23:04:10,489 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 23:04:10,491 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 23:04:10,495 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 23:04:10,497 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 23:04:10,498 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 23:04:10,500 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 23:04:10,501 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 23:04:10,505 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 23:04:10,507 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 23:04:10,508 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 23:04:10,510 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 23:04:10,513 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 23:04:10,515 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 23:04:10,517 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 23:04:10,519 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_g395h_f290lp_nrs1_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 23:04:11,107 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_g395h_f290lp_nrs1_uncal.fits',).
2021-05-17 23:04:11,119 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 23:04:11,388 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_g395h_f290lp_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 23:04:11,400 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0088.fits'.
2021-05-17 23:04:11,403 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits'.
2021-05-17 23:04:11,405 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0022.fits'.
2021-05-17 23:04:11,407 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2021-05-17 23:04:11,409 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 23:04:11,410 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2021-05-17 23:04:11,412 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0019.fits'.
2021-05-17 23:04:11,414 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 23:04:11,414 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 23:04:11,415 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0027.fits'.
2021-05-17 23:04:11,417 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0117.fits'.
2021-05-17 23:04:11,420 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 23:04:11,421 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 23:04:11,422 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 23:04:12,982 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:04:12,984 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:04:13,909 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 23:04:13,911 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 23:04:13,912 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 23:04:14,825 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:04:14,828 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:04:14,852 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2021-05-17 23:04:15,899 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 23:04:16,920 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:04:16,922 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:04:16,945 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0027.fits
2021-05-17 23:04:19,547 - stpipe.Detector1Pipeline.saturation - INFO - Detected 131958 saturated pixels
2021-05-17 23:04:19,687 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 23:04:19,719 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 23:04:20,724 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:04:20,727 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:04:20,728 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 23:04:20,730 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 23:04:21,660 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:04:21,662 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:04:21,686 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0117.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-05-17 23:04:22,837 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 23:04:23,852 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:04:23,855 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 23:04:23,880 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0019.fits
2021-05-17 23:05:38,115 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 23:05:39,348 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:05:39,351 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:05:39,383 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0022.fits
2021-05-17 23:05:39,528 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2021-05-17 23:05:41,660 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 23:05:42,678 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:05:42,680 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 23:05:43,194 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0088.fits
2021-05-17 23:05:47,720 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=20, nframes=1, groupgap=0
2021-05-17 23:05:47,722 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-05-17 23:05:49,158 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 23:05:50,865 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:05:50,868 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 23:05:51,180 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-05-17 23:05:51,423 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits
2021-05-17 23:05:51,679 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-05-17 23:05:51,734 - stpipe.Detector1Pipeline.jump - INFO - Found 32 possible cores to use for jump detection
2021-05-17 23:05:52,739 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-05-17 23:05:53,693 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-05-17 23:05:57,992 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 86673 pixels with at least one CR
2021-05-17 23:06:04,531 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 11.79 sec
2021-05-17 23:06:04,535 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 13.354949
2021-05-17 23:06:04,540 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 23:06:05,607 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:06:05,609 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 23:06:06,093 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2021-05-17 23:06:06,162 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits
2021-05-17 23:06:06,188 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 23:06:06,189 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:872: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int,:,:,:] *= ( segs_4[num_int,:,:,:] > 0)
2021-05-17 23:08:56,117 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 20
2021-05-17 23:08:56,119 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-05-17 23:08:56,255 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 23:08:57,228 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:08:57,231 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:08:57,295 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2021-05-17 23:08:57,307 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 23:08:57,738 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:08:57,741 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:08:57,833 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2021-05-17 23:08:57,845 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 23:08:57,847 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 23:08:57,849 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 23:08:57,860 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 23:08:58,420 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:08:58,423 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 23:08:58,626 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-05-17 23:08:58,627 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-05-17 23:08:58,629 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-05-17 23:08:58,630 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 23:09:02,036 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 23:10:12,422 - stpipe.AssignWcsStep - INFO - Update S_REGION to POLYGON ICRS 156.176999392 -45.687618156 156.178775679 -45.687618156 156.178775679 -45.686331563 156.176999392 -45.686331563
2021-05-17 23:10:12,423 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 23:10:12,429 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 23:10:12,442 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-05-17 23:10:14,351 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:10:14,360 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 23:10:14,388 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-05-17 23:10:14,391 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-05-17 23:10:14,571 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-05-17 23:10:14,572 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-05-17 23:10:14,573 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-05-17 23:10:14,574 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-05-17 23:10:14,585 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2021-05-17 23:10:14,718 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-05-17 23:10:14,764 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-05-17 23:10:14,794 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-05-17 23:10:14,886 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-05-17 23:10:14,918 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
2021-05-17 23:10:29,321 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-05-17 23:10:29,337 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 23:10:30,105 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:10:30,110 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 23:10:30,120 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_IFU
2021-05-17 23:10:30,121 - stpipe.SourceTypeStep - INFO - Input SRCTYAPT = UNKNOWN
2021-05-17 23:10:30,122 - stpipe.SourceTypeStep - INFO - Input source type is unknown; setting default SRCTYPE = EXTENDED
2021-05-17 23:10:30,124 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 23:10:30,135 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 23:10:30,598 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:10:30,601 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 23:10:30,609 - stpipe.WavecorrStep - INFO - Skipping wavecorr correction for EXP_TYPE NRS_IFU
2021-05-17 23:10:30,611 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 23:10:30,622 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 23:10:31,086 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:10:31,088 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 23:18:19,890 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 23:18:19,904 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 23:18:21,257 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2021-05-17 23:18:21,264 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 23:18:21,291 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0003.fits
2021-05-17 23:18:21,322 - stpipe.PathLossStep - INFO - Input exposure type is NRS_IFU
2021-05-17 23:19:32,581 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for IFU... Checking if files exist and obtaining datamodels. This takes a few minutes... from datamodel --> Detector: NRS1 Grating: G395H Filter: F290LP Lamp: REF EXP_TYPE: NRS_IFU Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0003.fits got input slices PLCOR_REF.shape (21, 21, 21) Looping through the slices... working with slice 0 SHAPES (52, 1775) (51, 1774) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V6 final left 780, right 831, top 2048, bottom 274 NEW SHAPE OF SLICE: (51, 1774) and corr_vals.shape: (51, 1774)
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_ifu_uni.py:168: RuntimeWarning: invalid value encountered in true_divide pathloss_divided = comp_sci/previous_sci
working with slice 1 SHAPES (52, 1737) (53, 1737) ALTERED SHAPE OF SLICE: V4 final left 1195, right 1248, top 2048, bottom 311 NEW SHAPE OF SLICE: (53, 1737) and corr_vals.shape: (53, 1737)
working with slice 2 SHAPES (51, 1779) (52, 1778) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V6 final left 729, right 781, top 2048, bottom 270 NEW SHAPE OF SLICE: (52, 1778) and corr_vals.shape: (52, 1778)
working with slice 3 SHAPES (52, 1733) (53, 1732) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V6 final left 1244, right 1297, top 2048, bottom 316 NEW SHAPE OF SLICE: (53, 1732) and corr_vals.shape: (53, 1732)
working with slice 4 SHAPES (51, 1783) (52, 1783) ALTERED SHAPE OF SLICE: V4 final left 680, right 732, top 2048, bottom 265 NEW SHAPE OF SLICE: (52, 1783) and corr_vals.shape: (52, 1783)
working with slice 5 SHAPES (53, 1728) (52, 1728) ALTERED SHAPE OF SLICE: V2 final left 1295, right 1347, top 2048, bottom 320 NEW SHAPE OF SLICE: (52, 1728) and corr_vals.shape: (52, 1728)
working with slice 6 SHAPES (52, 1787) (51, 1787) ALTERED SHAPE OF SLICE: V2 final left 632, right 683, top 2048, bottom 261 NEW SHAPE OF SLICE: (51, 1787) and corr_vals.shape: (51, 1787)
working with slice 7 SHAPES (53, 1723) (52, 1723) ALTERED SHAPE OF SLICE: V2 final left 1344, right 1396, top 2048, bottom 325 NEW SHAPE OF SLICE: (52, 1723) and corr_vals.shape: (52, 1723)
working with slice 8 SHAPES (52, 1791) (51, 1791) ALTERED SHAPE OF SLICE: V2 final left 583, right 634, top 2048, bottom 257 NEW SHAPE OF SLICE: (51, 1791) and corr_vals.shape: (51, 1791)
working with slice 9 SHAPES (53, 1719) (53, 1718) ALTERED SHAPE OF SLICE: V6 final left 1392, right 1445, top 2048, bottom 330 NEW SHAPE OF SLICE: (53, 1718) and corr_vals.shape: (53, 1718)
working with slice 10 SHAPES (51, 1795) (52, 1795) ALTERED SHAPE OF SLICE: V4 final left 532, right 584, top 2048, bottom 253 NEW SHAPE OF SLICE: (52, 1795) and corr_vals.shape: (52, 1795)
working with slice 11 SHAPES (53, 1714) (54, 1713) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V6 final left 1440, right 1494, top 2048, bottom 335 NEW SHAPE OF SLICE: (54, 1713) and corr_vals.shape: (54, 1713)
working with slice 12 SHAPES (51, 1799) (51, 1799)
working with slice 13 SHAPES (54, 1709) (54, 1709)
working with slice 14 SHAPES (52, 1803) (51, 1803) ALTERED SHAPE OF SLICE: V2 final left 435, right 486, top 2048, bottom 245 NEW SHAPE OF SLICE: (51, 1803) and corr_vals.shape: (51, 1803)
working with slice 15 SHAPES (54, 1704) (54, 1704)
working with slice 16 SHAPES (51, 1807) (52, 1807) ALTERED SHAPE OF SLICE: V4 final left 384, right 436, top 2048, bottom 241 NEW SHAPE OF SLICE: (52, 1807) and corr_vals.shape: (52, 1807)
working with slice 17 SHAPES (54, 1699) (54, 1699)
working with slice 18 SHAPES (51, 1811) (52, 1811) ALTERED SHAPE OF SLICE: V4 final left 335, right 387, top 2048, bottom 237 NEW SHAPE OF SLICE: (52, 1811) and corr_vals.shape: (52, 1811)
working with slice 19 SHAPES (55, 1695) (54, 1694) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V6 final left 1637, right 1691, top 2048, bottom 354 NEW SHAPE OF SLICE: (54, 1694) and corr_vals.shape: (54, 1694)
working with slice 20 SHAPES (52, 1815) (51, 1814) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V6 final left 287, right 338, top 2048, bottom 234 NEW SHAPE OF SLICE: (51, 1814) and corr_vals.shape: (51, 1814)
working with slice 21 SHAPES (55, 1690) (54, 1689) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V6 final left 1686, right 1740, top 2048, bottom 359 NEW SHAPE OF SLICE: (54, 1689) and corr_vals.shape: (54, 1689)
working with slice 22 SHAPES (51, 1819) (52, 1818) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V6 final left 236, right 288, top 2048, bottom 230 NEW SHAPE OF SLICE: (52, 1818) and corr_vals.shape: (52, 1818)
working with slice 23 SHAPES (55, 1685) (55, 1684) ALTERED SHAPE OF SLICE: V6 final left 1734, right 1789, top 2048, bottom 364 NEW SHAPE OF SLICE: (55, 1684) and corr_vals.shape: (55, 1684)
working with slice 24 SHAPES (51, 1823) (51, 1822) ALTERED SHAPE OF SLICE: V6 final left 188, right 239, top 2048, bottom 226 NEW SHAPE OF SLICE: (51, 1822) and corr_vals.shape: (51, 1822)
working with slice 25 SHAPES (55, 1680) (56, 1679) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V6 final left 1782, right 1838, top 2048, bottom 369 NEW SHAPE OF SLICE: (56, 1679) and corr_vals.shape: (56, 1679)
working with slice 26 SHAPES (51, 1826) (51, 1826)
working with slice 27 SHAPES (55, 1675) (56, 1674) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V6 final left 1831, right 1887, top 2048, bottom 374 NEW SHAPE OF SLICE: (56, 1674) and corr_vals.shape: (56, 1674)
working with slice 28 SHAPES (51, 1830) (51, 1830)
working with slice 29 SHAPES (56, 1669) (56, 1669)
Calculating statistics...
Absolute Difference : mean = 0.000e+00 median = 0.000e+00 stdev = 0.000e+00
Maximum AbsoluteDifference = 0.000e+00
Minimum AbsoluteDifference = 0.000e+00
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final result of pathloss test is PASSED ***
('* Script ifu_uni.py took ', '1.6062679807345073 minutes to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
Testing files for detector: nrs2
Working with uncal_file: /data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_g395h_f290lp_nrs2_uncal.fits
2021-05-17 23:21:13,427 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2021-05-17 23:21:13,454 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2021-05-17 23:21:13,456 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2021-05-17 23:21:13,458 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2021-05-17 23:21:13,460 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2021-05-17 23:21:13,462 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2021-05-17 23:21:13,464 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2021-05-17 23:21:13,466 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2021-05-17 23:21:13,468 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2021-05-17 23:21:13,470 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2021-05-17 23:21:13,472 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2021-05-17 23:21:13,474 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2021-05-17 23:21:13,475 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2021-05-17 23:21:13,477 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2021-05-17 23:21:13,479 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2021-05-17 23:21:13,481 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2021-05-17 23:21:13,483 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2021-05-17 23:21:13,489 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stpipe/step.py:359: ResourceWarning: unclosed file <_io.FileIO name='/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_g395h_f290lp_nrs2_uncal.fits' mode='rb' closefd=True>
gc.collect()
2021-05-17 23:21:14,676 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44/ifu_g395h_f290lp_nrs2_uncal.fits',).
2021-05-17 23:21:14,691 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2021-05-17 23:21:15,001 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_g395h_f290lp_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2021-05-17 23:21:15,015 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0085.fits'.
2021-05-17 23:21:15,017 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0020.fits'.
2021-05-17 23:21:15,019 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0025.fits'.
2021-05-17 23:21:15,022 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits'.
2021-05-17 23:21:15,024 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2021-05-17 23:21:15,025 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits'.
2021-05-17 23:21:15,027 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0018.fits'.
2021-05-17 23:21:15,030 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2021-05-17 23:21:15,030 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2021-05-17 23:21:15,031 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0026.fits'.
2021-05-17 23:21:15,034 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0118.fits'.
2021-05-17 23:21:15,036 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2021-05-17 23:21:15,037 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2021-05-17 23:21:15,038 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2021-05-17 23:21:16,595 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:21:16,598 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:21:17,427 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2021-05-17 23:21:17,428 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2021-05-17 23:21:17,430 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2021-05-17 23:21:17,948 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:21:17,953 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:21:17,979 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0011.fits
2021-05-17 23:21:19,019 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2021-05-17 23:21:19,666 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:21:19,669 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:21:19,690 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0026.fits
2021-05-17 23:21:22,123 - stpipe.Detector1Pipeline.saturation - INFO - Detected 151502 saturated pixels
2021-05-17 23:21:22,228 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2021-05-17 23:21:22,249 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2021-05-17 23:21:23,195 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:21:23,197 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:21:23,198 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2021-05-17 23:21:23,200 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2021-05-17 23:21:24,151 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:21:24,153 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:21:24,177 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0118.fits
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/stdatamodels/validate.py:34: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']
Failed validating 'enum' in schema:
OrderedDict([('title', 'Readout pattern'),
('type', 'string'),
('enum',
['ACQ1',
'ACQ2',
'BRIGHT1',
'BRIGHT2',
'DEEP2',
'DEEP8',
'FAST',
'FASTGRPAVG',
'FASTGRPAVG8',
'FASTGRPAVG16',
'FASTGRPAVG32',
'FASTGRPAVG64',
'FASTR1',
'FASTR100',
'FGS',
'FGS60',
'FGS8370',
'FGS840',
'FGSRAPID',
'FINEGUIDE',
'ID',
'MEDIUM2',
'MEDIUM8',
'NIS',
'NISRAPID',
'NRS',
'NRSIRS2',
'NRSN16R4',
'NRSN32R8',
'NRSN8R2',
'NRSRAPID',
'NRSIRS2RAPID',
'NRSRAPIDD1',
'NRSRAPIDD2',
'NRSRAPIDD6',
'NRSSLOW',
'RAPID',
'SHALLOW2',
'SHALLOW4',
'SLOW',
'SLOWR1',
'TRACK',
'ANY',
'N/A']),
('fits_ke ...
warnings.warn(errmsg, ValidationWarning)
2021-05-17 23:21:25,458 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2021-05-17 23:21:26,523 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:21:26,526 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2021-05-17 23:21:26,549 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0018.fits
2021-05-17 23:22:31,698 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2021-05-17 23:22:32,852 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:22:32,854 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:22:32,884 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0025.fits
2021-05-17 23:22:33,014 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2021-05-17 23:22:35,151 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2021-05-17 23:22:36,239 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:22:36,241 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'dark_output': None}
2021-05-17 23:22:36,722 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0085.fits
2021-05-17 23:22:40,986 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=20, nframes=1, groupgap=0
2021-05-17 23:22:40,987 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2021-05-17 23:22:42,350 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2021-05-17 23:22:44,058 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:22:44,061 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'rejection_threshold': 4.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 200.0, 'min_jump_to_flag_neighbors': 10.0}
2021-05-17 23:22:44,307 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2021-05-17 23:22:44,577 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0020.fits
2021-05-17 23:22:44,815 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-05-17 23:22:44,874 - stpipe.Detector1Pipeline.jump - INFO - Found 32 possible cores to use for jump detection
2021-05-17 23:22:45,840 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2021-05-17 23:22:46,731 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
2021-05-17 23:22:50,904 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier Two-point found 83533 pixels with at least one CR
2021-05-17 23:22:58,246 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 12.405 sec
2021-05-17 23:22:58,250 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 13.943646
2021-05-17 23:22:58,255 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2021-05-17 23:22:59,392 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:22:59,395 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'none'}
2021-05-17 23:22:59,996 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0017.fits
2021-05-17 23:23:00,051 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0020.fits
2021-05-17 23:23:00,076 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2021-05-17 23:23:00,077 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/jwst/ramp_fitting/ramp_fit.py:872: RuntimeWarning: invalid value encountered in multiply
var_p4[num_int,:,:,:] *= ( segs_4[num_int,:,:,:] > 0)
2021-05-17 23:25:47,240 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 20
2021-05-17 23:25:47,241 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2021-05-17 23:25:47,462 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2021-05-17 23:25:48,447 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:25:48,450 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:25:48,534 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2021-05-17 23:25:48,547 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 23:25:49,058 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:25:49,060 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp66z1io44'}
2021-05-17 23:25:49,143 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2021-05-17 23:25:49,156 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2021-05-17 23:25:49,158 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2021-05-17 23:25:49,160 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2021-05-17 23:25:49,171 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2021-05-17 23:25:49,788 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:25:49,793 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2021-05-17 23:25:50,014 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-05-17 23:25:50,015 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-05-17 23:25:50,016 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-05-17 23:25:50,018 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2021-05-17 23:25:53,622 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/gwcs/geometry.py:203: RuntimeWarning: invalid value encountered in remainder
lon = np.mod(lon, 360.0 * u.deg if nquant else 360.0)
2021-05-17 23:27:13,666 - stpipe.AssignWcsStep - INFO - Update S_REGION to POLYGON ICRS 156.176996289 -45.687617183 156.178772625 -45.687617183 156.178772625 -45.686330364 156.176996289 -45.686330364
2021-05-17 23:27:13,667 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2021-05-17 23:27:13,674 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2021-05-17 23:27:13,686 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2021-05-17 23:27:14,678 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:27:14,683 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 23:27:14,708 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2021-05-17 23:27:14,710 - stpipe.JwstStep - INFO - JwstStep instance created.
2021-05-17 23:27:14,850 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2021-05-17 23:27:14,851 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2021-05-17 23:27:14,851 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2021-05-17 23:27:14,853 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2021-05-17 23:27:14,863 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2021-05-17 23:27:14,987 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2021-05-17 23:27:15,030 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2021-05-17 23:27:15,058 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2021-05-17 23:27:15,137 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2021-05-17 23:27:15,165 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
2021-05-17 23:27:30,569 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2021-05-17 23:27:30,580 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2021-05-17 23:27:31,328 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:27:31,333 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 23:27:31,341 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_IFU
2021-05-17 23:27:31,342 - stpipe.SourceTypeStep - INFO - Input SRCTYAPT = UNKNOWN
2021-05-17 23:27:31,343 - stpipe.SourceTypeStep - INFO - Input source type is unknown; setting default SRCTYPE = EXTENDED
2021-05-17 23:27:31,344 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2021-05-17 23:27:31,354 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2021-05-17 23:27:31,826 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:27:31,828 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2021-05-17 23:27:31,837 - stpipe.WavecorrStep - INFO - Skipping wavecorr correction for EXP_TYPE NRS_IFU
2021-05-17 23:27:31,839 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2021-05-17 23:27:31,850 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2021-05-17 23:27:32,340 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:27:32,342 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2021-05-17 23:34:56,159 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2021-05-17 23:34:56,183 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2021-05-17 23:34:57,511 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs2_uncal.fits>,).
2021-05-17 23:34:57,517 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2021-05-17 23:34:57,544 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0003.fits
2021-05-17 23:34:57,569 - stpipe.PathLossStep - INFO - Input exposure type is NRS_IFU
2021-05-17 23:36:07,772 - stpipe.PathLossStep - INFO - Step PathLossStep done
Running test for IFU... Checking if files exist and obtaining datamodels. This takes a few minutes... from datamodel --> Detector: NRS2 Grating: G395H Filter: F290LP Lamp: REF EXP_TYPE: NRS_IFU Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0003.fits got input slices PLCOR_REF.shape (21, 21, 21) Looping through the slices... working with slice 0 SHAPES (52, 1677) (51, 1677) ALTERED SHAPE OF SLICE: V2 final left 780, right 831, top 1677, bottom 0 NEW SHAPE OF SLICE: (51, 1677) and corr_vals.shape: (51, 1677)
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_ifu_uni.py:168: RuntimeWarning: invalid value encountered in true_divide pathloss_divided = comp_sci/previous_sci
working with slice 1 SHAPES (52, 1721) (53, 1722) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V8 final left 1195, right 1248, top 1721, bottom -1 NEW SHAPE OF SLICE: (53, 0) and corr_vals.shape: (53, 1722) ALTERED SHAPE OF SLICE: V7 final left 1195, right 1248, top 1722, bottom -2 NEW SHAPE OF SLICE: (53, 0) and corr_vals.shape: (53, 1722) ALTERED SHAPE OF SLICE: V7 final left 1195, right 1248, top 1723, bottom -3 NEW SHAPE OF SLICE: (53, 0) and corr_vals.shape: (53, 1722) ALTERED SHAPE OF SLICE: V7 final left 1195, right 1248, top 1724, bottom -4 NEW SHAPE OF SLICE: (53, 0) and corr_vals.shape: (53, 1722) ALTERED SHAPE OF SLICE: V7 final left 1195, right 1248, top 1725, bottom -5 NEW SHAPE OF SLICE: (53, 0) and corr_vals.shape: (53, 1722) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V7 final left 1195, right 1248, top 1726, bottom -6 NEW SHAPE OF SLICE: (53, 0) and corr_vals.shape: (53, 1722) shapes did not match! full_cut2slice: (53, 0), corr_vals (53, 1722) working with slice 2 SHAPES (51, 1672) (52, 1672) ALTERED SHAPE OF SLICE: V4 final left 729, right 781, top 1672, bottom 0 NEW SHAPE OF SLICE: (52, 1672) and corr_vals.shape: (52, 1672)
working with slice 3 SHAPES (52, 1726) (52, 1727) ALTERED SHAPE OF SLICE: V8 final left 1245, right 1297, top 1726, bottom -1 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1727) ALTERED SHAPE OF SLICE: V8 final left 1245, right 1297, top 1726, bottom -2 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1727) ALTERED SHAPE OF SLICE: V8 final left 1245, right 1297, top 1726, bottom -3 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1727) ALTERED SHAPE OF SLICE: V8 final left 1245, right 1297, top 1726, bottom -4 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1727) ALTERED SHAPE OF SLICE: V8 final left 1245, right 1297, top 1726, bottom -5 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1727) ALTERED SHAPE OF SLICE: V8 final left 1245, right 1297, top 1726, bottom -6 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1727) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V8 final left 1245, right 1297, top 1726, bottom -7 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1727) shapes did not match! full_cut2slice: (52, 0), corr_vals (52, 1727) working with slice 4 SHAPES (51, 1667) (52, 1667) ALTERED SHAPE OF SLICE: V4 final left 680, right 732, top 1667, bottom 0 NEW SHAPE OF SLICE: (52, 1667) and corr_vals.shape: (52, 1667)
working with slice 5 SHAPES (53, 1732) (52, 1732) ALTERED SHAPE OF SLICE: V2 final left 1295, right 1347, top 1732, bottom 0 NEW SHAPE OF SLICE: (52, 1732) and corr_vals.shape: (52, 1732)
working with slice 6 SHAPES (52, 1662) (51, 1663) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V8 final left 632, right 683, top 1662, bottom -1 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1663) ALTERED SHAPE OF SLICE: V8 final left 632, right 683, top 1662, bottom -2 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1663) ALTERED SHAPE OF SLICE: V8 final left 632, right 683, top 1662, bottom -3 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1663) ALTERED SHAPE OF SLICE: V8 final left 632, right 683, top 1662, bottom -4 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1663) ALTERED SHAPE OF SLICE: V8 final left 632, right 683, top 1662, bottom -5 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1663) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V8 final left 632, right 683, top 1662, bottom -6 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1663) shapes did not match! full_cut2slice: (51, 0), corr_vals (51, 1663) working with slice 7 SHAPES (53, 1737) (52, 1738) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V8 final left 1344, right 1396, top 1737, bottom -1 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1738) ALTERED SHAPE OF SLICE: V7 final left 1344, right 1396, top 1738, bottom -2 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1738) ALTERED SHAPE OF SLICE: V7 final left 1344, right 1396, top 1739, bottom -3 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1738) ALTERED SHAPE OF SLICE: V7 final left 1344, right 1396, top 1740, bottom -4 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1738) ALTERED SHAPE OF SLICE: V7 final left 1344, right 1396, top 1741, bottom -5 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1738) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V7 final left 1344, right 1396, top 1742, bottom -6 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1738) shapes did not match! full_cut2slice: (52, 0), corr_vals (52, 1738) working with slice 8 SHAPES (52, 1657) (51, 1658) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V8 final left 583, right 634, top 1657, bottom -1 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1658) ALTERED SHAPE OF SLICE: V7 final left 583, right 634, top 1658, bottom -2 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1658) ALTERED SHAPE OF SLICE: V7 final left 583, right 634, top 1659, bottom -3 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1658) ALTERED SHAPE OF SLICE: V7 final left 583, right 634, top 1660, bottom -4 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1658) ALTERED SHAPE OF SLICE: V7 final left 583, right 634, top 1661, bottom -5 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1658) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V7 final left 583, right 634, top 1662, bottom -6 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1658) shapes did not match! full_cut2slice: (51, 0), corr_vals (51, 1658) working with slice 9 SHAPES (53, 1743) (53, 1743)
working with slice 10 SHAPES (51, 1653) (52, 1653) ALTERED SHAPE OF SLICE: V4 final left 532, right 584, top 1653, bottom 0 NEW SHAPE OF SLICE: (52, 1653) and corr_vals.shape: (52, 1653)
working with slice 11 SHAPES (53, 1749) (53, 1749)
working with slice 12 SHAPES (51, 1648) (52, 1648) ALTERED SHAPE OF SLICE: V4 final left 483, right 535, top 1648, bottom 0 NEW SHAPE OF SLICE: (52, 1648) and corr_vals.shape: (52, 1648)
working with slice 13 SHAPES (54, 1754) (54, 1755) ALTERED SHAPE OF SLICE: V8 final left 1490, right 1544, top 1754, bottom -1 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1755) ALTERED SHAPE OF SLICE: V8 final left 1490, right 1544, top 1754, bottom -2 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1755) ALTERED SHAPE OF SLICE: V8 final left 1490, right 1544, top 1754, bottom -3 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1755) ALTERED SHAPE OF SLICE: V8 final left 1490, right 1544, top 1754, bottom -4 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1755) ALTERED SHAPE OF SLICE: V8 final left 1490, right 1544, top 1754, bottom -5 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1755) ALTERED SHAPE OF SLICE: V8 final left 1490, right 1544, top 1754, bottom -6 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1755) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V8 final left 1490, right 1544, top 1754, bottom -7 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1755) shapes did not match! full_cut2slice: (54, 0), corr_vals (54, 1755) working with slice 14 SHAPES (52, 1643) (51, 1644) ALTERED SHAPE OF SLICE: V2 ALTERED SHAPE OF SLICE: V8 final left 435, right 486, top 1643, bottom -1 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1644) ALTERED SHAPE OF SLICE: V7 final left 435, right 486, top 1644, bottom -2 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1644) ALTERED SHAPE OF SLICE: V7 final left 435, right 486, top 1645, bottom -3 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1644) ALTERED SHAPE OF SLICE: V7 final left 435, right 486, top 1646, bottom -4 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1644) ALTERED SHAPE OF SLICE: V7 final left 435, right 486, top 1647, bottom -5 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1644) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V7 final left 435, right 486, top 1648, bottom -6 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1644) shapes did not match! full_cut2slice: (51, 0), corr_vals (51, 1644) working with slice 15 SHAPES (54, 1760) (54, 1761) ALTERED SHAPE OF SLICE: V8 final left 1539, right 1593, top 1760, bottom -1 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1761) ALTERED SHAPE OF SLICE: V8 final left 1539, right 1593, top 1760, bottom -2 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1761) ALTERED SHAPE OF SLICE: V8 final left 1539, right 1593, top 1760, bottom -3 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1761) ALTERED SHAPE OF SLICE: V8 final left 1539, right 1593, top 1760, bottom -4 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1761) ALTERED SHAPE OF SLICE: V8 final left 1539, right 1593, top 1760, bottom -5 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1761) ALTERED SHAPE OF SLICE: V8 final left 1539, right 1593, top 1760, bottom -6 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1761) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V8 final left 1539, right 1593, top 1760, bottom -7 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1761) shapes did not match! full_cut2slice: (54, 0), corr_vals (54, 1761) working with slice 16 SHAPES (51, 1639) (51, 1639)
working with slice 17 SHAPES (54, 1766) (54, 1767) ALTERED SHAPE OF SLICE: V8 final left 1588, right 1642, top 1766, bottom -1 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1767) ALTERED SHAPE OF SLICE: V8 final left 1588, right 1642, top 1766, bottom -2 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1767) ALTERED SHAPE OF SLICE: V8 final left 1588, right 1642, top 1766, bottom -3 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1767) ALTERED SHAPE OF SLICE: V8 final left 1588, right 1642, top 1766, bottom -4 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1767) ALTERED SHAPE OF SLICE: V8 final left 1588, right 1642, top 1766, bottom -5 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1767) ALTERED SHAPE OF SLICE: V8 final left 1588, right 1642, top 1766, bottom -6 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1767) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V8 final left 1588, right 1642, top 1766, bottom -7 NEW SHAPE OF SLICE: (54, 0) and corr_vals.shape: (54, 1767) shapes did not match! full_cut2slice: (54, 0), corr_vals (54, 1767) working with slice 18 SHAPES (51, 1634) (52, 1635) ALTERED SHAPE OF SLICE: V4 ALTERED SHAPE OF SLICE: V8 final left 335, right 387, top 1634, bottom -1 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1635) ALTERED SHAPE OF SLICE: V8 final left 335, right 387, top 1634, bottom -2 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1635) ALTERED SHAPE OF SLICE: V8 final left 335, right 387, top 1634, bottom -3 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1635) ALTERED SHAPE OF SLICE: V8 final left 335, right 387, top 1634, bottom -4 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1635) ALTERED SHAPE OF SLICE: V8 final left 335, right 387, top 1634, bottom -5 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1635) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V8 final left 335, right 387, top 1634, bottom -6 NEW SHAPE OF SLICE: (52, 0) and corr_vals.shape: (52, 1635) shapes did not match! full_cut2slice: (52, 0), corr_vals (52, 1635) working with slice 19 SHAPES (55, 1772) (54, 1772) ALTERED SHAPE OF SLICE: V2 final left 1637, right 1691, top 1772, bottom 0 NEW SHAPE OF SLICE: (54, 1772) and corr_vals.shape: (54, 1772)
working with slice 20 SHAPES (52, 1630) (51, 1630) ALTERED SHAPE OF SLICE: V2 final left 287, right 338, top 1630, bottom 0 NEW SHAPE OF SLICE: (51, 1630) and corr_vals.shape: (51, 1630)
working with slice 21 SHAPES (55, 1778) (55, 1778)
working with slice 22 SHAPES (51, 1625) (51, 1626) ALTERED SHAPE OF SLICE: V8 final left 237, right 288, top 1625, bottom -1 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1626) ALTERED SHAPE OF SLICE: V7 final left 237, right 288, top 1626, bottom -2 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1626) ALTERED SHAPE OF SLICE: V7 final left 237, right 288, top 1627, bottom -3 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1626) ALTERED SHAPE OF SLICE: V7 final left 237, right 288, top 1628, bottom -4 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1626) ALTERED SHAPE OF SLICE: V7 final left 237, right 288, top 1629, bottom -5 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1626) ALTERED SHAPE OF SLICE: V7 final left 237, right 288, top 1630, bottom -6 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1626) WARNING: may be in infinite loop! ALTERED SHAPE OF SLICE: V7 final left 237, right 288, top 1631, bottom -7 NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1626) shapes did not match! full_cut2slice: (51, 0), corr_vals (51, 1626) working with slice 23 SHAPES (55, 1784) (55, 1784)
working with slice 24 SHAPES (51, 1621) (52, 1621) ALTERED SHAPE OF SLICE: V4 final left 187, right 239, top 1621, bottom 0 NEW SHAPE OF SLICE: (52, 1621) and corr_vals.shape: (52, 1621)
working with slice 25 SHAPES (55, 1790) (56, 1790) ALTERED SHAPE OF SLICE: V4 final left 1782, right 1838, top 1790, bottom 0 NEW SHAPE OF SLICE: (56, 1790) and corr_vals.shape: (56, 1790)
working with slice 26 SHAPES (52, 1617) (51, 1617) ALTERED SHAPE OF SLICE: V2 final left 139, right 190, top 1617, bottom 0 NEW SHAPE OF SLICE: (51, 1617) and corr_vals.shape: (51, 1617)
working with slice 27
SHAPES (55, 1796) (56, 1797)
ALTERED SHAPE OF SLICE: V4
ALTERED SHAPE OF SLICE: V8
final left 1831, right 1887, top 1796, bottom -1
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1797)
ALTERED SHAPE OF SLICE: V8
final left 1831, right 1887, top 1796, bottom -2
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1797)
ALTERED SHAPE OF SLICE: V8
final left 1831, right 1887, top 1796, bottom -3
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1797)
ALTERED SHAPE OF SLICE: V8
final left 1831, right 1887, top 1796, bottom -4
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1797)
ALTERED SHAPE OF SLICE: V8
final left 1831, right 1887, top 1796, bottom -5
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1797)
WARNING: may be in infinite loop!
ALTERED SHAPE OF SLICE: V8
final left 1831, right 1887, top 1796, bottom -6
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1797)
shapes did not match! full_cut2slice: (56, 0), corr_vals (56, 1797)
working with slice 28
SHAPES (51, 1612) (51, 1613)
ALTERED SHAPE OF SLICE: V8
final left 89, right 140, top 1612, bottom -1
NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1613)
ALTERED SHAPE OF SLICE: V8
final left 89, right 140, top 1612, bottom -2
NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1613)
ALTERED SHAPE OF SLICE: V8
final left 89, right 140, top 1612, bottom -3
NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1613)
ALTERED SHAPE OF SLICE: V8
final left 89, right 140, top 1612, bottom -4
NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1613)
ALTERED SHAPE OF SLICE: V8
final left 89, right 140, top 1612, bottom -5
NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1613)
ALTERED SHAPE OF SLICE: V8
final left 89, right 140, top 1612, bottom -6
NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1613)
WARNING: may be in infinite loop!
ALTERED SHAPE OF SLICE: V8
final left 89, right 140, top 1612, bottom -7
NEW SHAPE OF SLICE: (51, 0) and corr_vals.shape: (51, 1613)
shapes did not match! full_cut2slice: (51, 0), corr_vals (51, 1613)
working with slice 29
SHAPES (56, 1802) (56, 1803)
ALTERED SHAPE OF SLICE: V8
final left 1880, right 1936, top 1802, bottom -1
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1803)
ALTERED SHAPE OF SLICE: V8
final left 1880, right 1936, top 1802, bottom -2
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1803)
ALTERED SHAPE OF SLICE: V8
final left 1880, right 1936, top 1802, bottom -3
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1803)
ALTERED SHAPE OF SLICE: V8
final left 1880, right 1936, top 1802, bottom -4
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1803)
ALTERED SHAPE OF SLICE: V8
final left 1880, right 1936, top 1802, bottom -5
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1803)
ALTERED SHAPE OF SLICE: V8
final left 1880, right 1936, top 1802, bottom -6
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1803)
WARNING: may be in infinite loop!
ALTERED SHAPE OF SLICE: V8
final left 1880, right 1936, top 1802, bottom -7
NEW SHAPE OF SLICE: (56, 0) and corr_vals.shape: (56, 1803)
shapes did not match! full_cut2slice: (56, 0), corr_vals (56, 1803)
Calculating statistics...
Absolute Difference : mean = 0.000e+00 median = 0.000e+00 stdev = 0.000e+00
Maximum AbsoluteDifference = 0.000e+00
Minimum AbsoluteDifference = 0.000e+00
Percentage of pixels where median of absolute differences is greater than:
-> 1xtheshold = 0%
-> 3xtheshold = 0%
-> 5xtheshold = 0%
*** Result of the test: PASSED
*** Final result of pathloss test is PASSED ***
('* Script ifu_uni.py took ', '1.3287201960881552 minutes to finish.')
Did pathloss validation test passed? All slits PASSED path_loss test.
# Quickly see if the test passed
print('These are the final results of the tests: ')
for key, val in results_dict.items():
print(key, val)
These are the final results of the tests: fs_prism_clear All slits PASSED path_loss test. fs_fullframe_g395h_f290lp All slits PASSED path_loss test. mos_prism_clear skipped mos_g140m_f100lp All slits PASSED path_loss test. ifu_prism_clear skipped ifu_g395h_f290lp All slits PASSED path_loss test.
/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.8/site-packages/ipykernel/ipkernel.py:283: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above. and should_run_async(code)
Author: Maria A. Pena-Guerrero, Staff Scientist II - Systems Science Support, NIRSpec
Updated On: Apr/9/2021